[Onetouch Idol 3 Android Development] SpaghettiCat:
BALLER! Success report for the newer OTA update:

Model: 6039Y

Firmware Build: 01007

Purchase Location: Germany

Desktop OS: Windows 7 SP1

I first tried the normal 8GB 6039Y image and that seemed to work fine:

Process Index:0
Programmer Path:C:\Users\myuser\Downloads\android\6039Y_8GB\prog_emmc_firehose_8916.mbn
Image Search Path:C:\Users\myuser\Downloads\android\6039Y_8GB
Please select the XML file
Start Download
Program Path:C:\Users\myuser\Downloads\android\6039Y_8GB\prog_emmc_firehose_8916.mbn
COM Port number:5
Sahara Connecting ...
Sahara Version:2
Start Sending Programmer
Sending Programmer Finished
Switch To FireHose
Max Payload Size to Target:49152 Bytes
Device Type:eMMC
Platform:8x26
Disable Ack Raw Data Every N Packets
Ack Raw Data:False
Skip Write:False
Always Validate:False
Use Verbose:False
COM Port number:5
Sending NOP
FireHose NOP sent successfully
Sending Configuration
Device Type:eMMC
Platform:8x26
Set TxBuffer 0x4000, RxBuffer 0x4000
Firehose configure packet sent successfully!
Total Bytes To Program 0x308680
Download Image
PROGRAM: Partition 0, Sector: 0, Length: 33 Sectors, Sector Size: 512 Bytes
File: C:\Users\myuser\Downloads\android\6039Y_8GB\gpt_backup0.bin
PROGRAM: Written Bytes 0x4200 (64)
Program Size: 0.02 MB
PROGRAM: Partition 0, Sector: 0, Length: 34 Sectors, Sector Size: 512 Bytes
File: C:\Users\myuser\Downloads\android\6039Y_8GB\gpt_main0.bin
PROGRAM: Written Bytes 0x4400 (64)
Program Size: 0.02 MB
PROGRAM: Partition 0, Sector: 398432, Length: 2048 Sectors, Sector Size: 512 Bytes
File: C:\Users\myuser\Downloads\android\6039Y_8GB\aboot.mbn
PROGRAM: Written Bytes 0x100000 (64)
Program Size: 1.00 MB
PROGRAM: Partition 0, Sector: 396384, Length: 2048 Sectors, Sector Size: 512 Bytes
File: C:\Users\myuser\Downloads\android\6039Y_8GB\aboot.mbn
PROGRAM: Written Bytes 0x100000 (64)
Program Size: 1.00 MB
PROGRAM: Partition 0, Sector: 274450, Length: 1024 Sectors, Sector Size: 512 Bytes
File: C:\Users\myuser\Downloads\android\6039Y_8GB\hyp.mbn
PROGRAM: Written Bytes 0x80000 (64)
Program Size: 0.50 MB
PROGRAM: Partition 0, Sector: 273426, Length: 1024 Sectors, Sector Size: 512 Bytes
File: C:\Users\myuser\Downloads\android\6039Y_8GB\hyp.mbn
PROGRAM: Written Bytes 0x80000 (64)
Program Size: 0.50 MB
PROGRAM: Partition 0, Sector: 272402, Length: 1024 Sectors, Sector Size: 512 Bytes
File: C:\Users\myuser\Downloads\android\6039Y_8GB\tz.mbn
PROGRAM: Written Bytes 0x80000 (64)
Program Size: 0.50 MB
PROGRAM: Partition 0, Sector: 271378, Length: 1024 Sectors, Sector Size: 512 Bytes
File: C:\Users\myuser\Downloads\android\6039Y_8GB\tz.mbn
PROGRAM: Written Bytes 0x80000 (64)
Program Size: 0.50 MB
PROGRAM: Partition 0, Sector: 270354, Length: 1024 Sectors, Sector Size: 512 Bytes
File: C:\Users\myuser\Downloads\android\6039Y_8GB\rpm.mbn
PROGRAM: Written Bytes 0x80000 (64)
Program Size: 0.50 MB
PROGRAM: Partition 0, Sector: 269330, Length: 1024 Sectors, Sector Size: 512 Bytes
File: C:\Users\myuser\Downloads\android\6039Y_8GB\rpm.mbn
PROGRAM: Written Bytes 0x80000 (64)
Program Size: 0.50 MB
PROGRAM: Partition 0, Sector: 268306, Length: 1024 Sectors, Sector Size: 512 Bytes
File: C:\Users\myuser\Downloads\android\6039Y_8GB\sbl1.mbn
PROGRAM: Written Bytes 0x80000 (64)
Program Size: 0.50 MB
PROGRAM: Partition 0, Sector: 267282, Length: 1024 Sectors, Sector Size: 512 Bytes
File: C:\Users\myuser\Downloads\android\6039Y_8GB\sbl1.mbn
PROGRAM: Written Bytes 0x80000 (64)
Program Size: 0.50 MB
Total Size: 6.03 MB
Total Size: 0 Seconds
PATCH: Partition 0, Sector: 1, Offset 48 Bytes, Size: 8 Bytes, Value: NUM_DISK_SECTORS-34.
PATCH: Partition 0, Sector: 0, Offset 48 Bytes, Size: 8 Bytes, Value: NUM_DISK_SECTORS-34.
PATCH: Partition 0, Sector: 1, Offset 32 Bytes, Size: 8 Bytes, Value: NUM_DISK_SECTORS-1.
PATCH: Partition 0, Sector: 0, Offset 24 Bytes, Size: 8 Bytes, Value: NUM_DISK_SECTORS-1.
PATCH: Partition 0, Sector: 0, Offset 72 Bytes, Size: 8 Bytes, Value: NUM_DISK_SECTORS-33.
PATCH: Partition 0, Sector: 1, Offset 88 Bytes, Size: 4 Bytes, Value: CRC32(2,5120)
PATCH: Partition 0, Sector: 0, Offset 88 Bytes, Size: 4 Bytes, Value: CRC32(NUM_DISK_SECTORS-33.,5120)
PATCH: Partition 0, Sector: 1, Offset 16 Bytes, Size: 4 Bytes, Value: 0
PATCH: Partition 0, Sector: 1, Offset 16 Bytes, Size: 4 Bytes, Value: CRC32(1,92)
PATCH: Partition 0, Sector: 0, Offset 16 Bytes, Size: 4 Bytes, Value: 0
PATCH: Partition 0, Sector: 0, Offset 16 Bytes, Size: 4 Bytes, Value: CRC32(NUM_DISK_SECTORS-1.,92)
Total download file size: 6.032715MB
Throughput: 0M/s
Reset Phone
Waiting for reset done...
Download Fail:FireHose Fail Fail to find QDLoader port after switch
Finish Download

Then I tried the repartitioned image and that had a similar log:

Programmer Path:C:\Users\myuser\Downloads\android\6039Y_repartitioned\prog_emmc_firehose_8916.mbn
Image Search Path:C:\Users\myuser\Downloads\android\6039Y_repartitioned
Please select the XML file
Start Download
Program Path:C:\Users\myuser\Downloads\android\6039Y_repartitioned\prog_emmc_firehose_8916.mbn
COM Port number:5
Sahara Connecting ...
Sahara Version:2
Start Sending Programmer
Sending Programmer Finished
Switch To FireHose
Max Payload Size to Target:49152 Bytes
Device Type:eMMC
Platform:8x26
Disable Ack Raw Data Every N Packets
Ack Raw Data:False
Skip Write:False
Always Validate:False
Use Verbose:False
COM Port number:5
Sending NOP
FireHose NOP sent successfully
Sending Configuration
Device Type:eMMC
Platform:8x26
Set TxBuffer 0x4000, RxBuffer 0x4000
Firehose configure packet sent successfully!
Total Bytes To Program 0x308680
Download Image
PROGRAM: Partition 0, Sector: 0, Length: 33 Sectors, Sector Size: 512 Bytes
File: C:\Users\myuser\Downloads\android\6039Y_repartitioned\gpt_backup0.bin
PROGRAM: Written Bytes 0x4200 (64)
Program Size: 0.02 MB
PROGRAM: Partition 0, Sector: 0, Length: 34 Sectors, Sector Size: 512 Bytes
File: C:\Users\myuser\Downloads\android\6039Y_repartitioned\gpt_main0.bin
PROGRAM: Written Bytes 0x4400 (64)
Program Size: 0.02 MB
PROGRAM: Partition 0, Sector: 398432, Length: 2048 Sectors, Sector Size: 512 Bytes
File: C:\Users\myuser\Downloads\android\6039Y_repartitioned\aboot.mbn
PROGRAM: Written Bytes 0x100000 (64)
Program Size: 1.00 MB
PROGRAM: Partition 0, Sector: 396384, Length: 2048 Sectors, Sector Size: 512 Bytes
File: C:\Users\myuser\Downloads\android\6039Y_repartitioned\aboot.mbn
PROGRAM: Written Bytes 0x100000 (64)
Program Size: 1.00 MB
PROGRAM: Partition 0, Sector: 274450, Length: 1024 Sectors, Sector Size: 512 Bytes
File: C:\Users\myuser\Downloads\android\6039Y_repartitioned\hyp.mbn
PROGRAM: Written Bytes 0x80000 (64)
Program Size: 0.50 MB
PROGRAM: Partition 0, Sector: 273426, Length: 1024 Sectors, Sector Size: 512 Bytes
File: C:\Users\myuser\Downloads\android\6039Y_repartitioned\hyp.mbn
PROGRAM: Written Bytes 0x80000 (64)
Program Size: 0.50 MB
PROGRAM: Partition 0, Sector: 272402, Length: 1024 Sectors, Sector Size: 512 Bytes
File: C:\Users\myuser\Downloads\android\6039Y_repartitioned\tz.mbn
PROGRAM: Written Bytes 0x80000 (64)
Program Size: 0.50 MB
PROGRAM: Partition 0, Sector: 271378, Length: 1024 Sectors, Sector Size: 512 Bytes
File: C:\Users\myuser\Downloads\android\6039Y_repartitioned\tz.mbn
PROGRAM: Written Bytes 0x80000 (64)
Program Size: 0.50 MB
PROGRAM: Partition 0, Sector: 270354, Length: 1024 Sectors, Sector Size: 512 Bytes
File: C:\Users\myuser\Downloads\android\6039Y_repartitioned\rpm.mbn
PROGRAM: Written Bytes 0x80000 (64)
Program Size: 0.50 MB
PROGRAM: Partition 0, Sector: 269330, Length: 1024 Sectors, Sector Size: 512 Bytes
File: C:\Users\myuser\Downloads\android\6039Y_repartitioned\rpm.mbn
PROGRAM: Written Bytes 0x80000 (64)
Program Size: 0.50 MB
PROGRAM: Partition 0, Sector: 268306, Length: 1024 Sectors, Sector Size: 512 Bytes
File: C:\Users\myuser\Downloads\android\6039Y_repartitioned\sbl1.mbn
PROGRAM: Written Bytes 0x80000 (64)
Program Size: 0.50 MB
PROGRAM: Partition 0, Sector: 267282, Length: 1024 Sectors, Sector Size: 512 Bytes
File: C:\Users\myuser\Downloads\android\6039Y_repartitioned\sbl1.mbn
PROGRAM: Written Bytes 0x80000 (64)
Program Size: 0.50 MB
Total Size: 6.03 MB
Total Size: 0 Seconds
PATCH: Partition 0, Sector: 1, Offset 48 Bytes, Size: 8 Bytes, Value: NUM_DISK_SECTORS-34.
PATCH: Partition 0, Sector: 0, Offset 48 Bytes, Size: 8 Bytes, Value: NUM_DISK_SECTORS-34.
PATCH: Partition 0, Sector: 1, Offset 32 Bytes, Size: 8 Bytes, Value: NUM_DISK_SECTORS-1.
PATCH: Partition 0, Sector: 0, Offset 24 Bytes, Size: 8 Bytes, Value: NUM_DISK_SECTORS-1.
PATCH: Partition 0, Sector: 0, Offset 72 Bytes, Size: 8 Bytes, Value: NUM_DISK_SECTORS-33.
PATCH: Partition 0, Sector: 1, Offset 88 Bytes, Size: 4 Bytes, Value: CRC32(2,5120)
PATCH: Partition 0, Sector: 0, Offset 88 Bytes, Size: 4 Bytes, Value: CRC32(NUM_DISK_SECTORS-33.,5120)
PATCH: Partition 0, Sector: 1, Offset 16 Bytes, Size: 4 Bytes, Value: 0
PATCH: Partition 0, Sector: 1, Offset 16 Bytes, Size: 4 Bytes, Value: CRC32(1,92)
PATCH: Partition 0, Sector: 0, Offset 16 Bytes, Size: 4 Bytes, Value: 0
PATCH: Partition 0, Sector: 0, Offset 16 Bytes, Size: 4 Bytes, Value: CRC32(NUM_DISK_SECTORS-1.,92)
Total download file size: 6.032715MB
Throughput: 0M/s
Reset Phone
Waiting for reset done...
Download Fail:FireHose Fail Fail to find QDLoader port after switch
Finish Download

Note that both have this error line at the end, but it didn't seem to cause a problem:

Although Petrov mentioned in the OP "you should have a repartitioned device at the end, and only the resize2fs command should be enough to start to utilize the whole memory chip " in "Settings -> Storage" it already shows the doubled available space without running that command, so I guess it's not necessary to run `resize2fs`?

Then when I install the custom TWRP recovery here is where I got stuck. What worked was (on Linux now):

adb reboot-bootloader
sudo fastboot -i 0x1bbb boot twrp_recovery-2.8.7.0-idol3-6039y.img

Note the `sudo` and note `-i 0x1bbb`. Even `sudo fastboot devices` won't list any devices for you unless you pass `-i 0x1bbb`! I don't know if it was necessary but I added the udev rules (url=https://wiki.cyanogenmod.org/w/UDEV).

Finally, I downloaded SuperSU onto the SD Card and installed that from TWRP.

Huge thank you to petrov and everyone else that contributed to this. You guys are great :)