[Miscellaneous Android Development] bigrammy:
Check your recovery log you will see it's backed up all the folders in there rather than clone the entire partitions (empty space) ;)

My Log Here. :good:

[BACKUP STARTED]
* Backup Folder: /external_sd/TWRP/BACKUPS/p6000/custom2015-03-12--14-12-47/
I:Estimated total time: 0
Estimated remaining time: 0
Backing up Custom Partition...
I:Creating backup...
I:Creating tar file '/external_sd/TWRP/BACKUPS/p6000/custom2015-03-12--14-12-47//custom.ext4.win'
I:addFile '/custom/app-res' including root: 0
setting selinux context: u:object_r:unlabeled:s0
I:addFile '/custom/app-res/SettingsProvider-res.apk' including root: 0
setting selinux context: u:object_r:unlabeled:s0
I:addFile '/custom/app-res/android-res.apk' including root: 0
setting selinux context: u:object_r:unlabeled:s0
I:addFile '/custom/app-res/launcher3-res.apk' including root: 0
setting selinux context: u:object_r:unlabeled:s0
I:addFile '/custom/app_unremoveable' including root: 0
setting selinux context: u:object_r:unlabeled:s0
I:addFile '/custom/app_unremoveable/Elephone.apk' including root: 0
setting selinux context: u:object_r:unlabeled:s0
I:addFile '/custom/app_unremoveable/Elephone_Launcher3_20131226.apk' including root: 0
setting selinux context: u:object_r:unlabeled:s0
I:addFile '/custom/app_unremoveable/Superuser.apk' including root: 0
setting selinux context: u:object_r:unlabeled:s0
I:addFile '/custom/bootani' including root: 0
setting selinux context: u:object_r:unlabeled:s0
I:addFile '/custom/bootani/bootanimation.zip' including root: 0
setting selinux context: u:object_r:unlabeled:s0
I:addFile '/custom/bootani/bootaudio.mp3' including root: 0
setting selinux context: u:object_r:unlabeled:s0
I:addFile '/custom/bootani/shutanimation.zip' including root: 0
setting selinux context: u:object_r:unlabeled:s0
I:addFile '/custom/cip-build.prop' including root: 0
setting selinux context: u:object_r:unlabeled:s0
I:addFile '/custom/customprop' including root: 0
setting selinux context: u:object_r:unlabeled:s0
I:addFile '/custom/customprop/custom.prop' including root: 0
setting selinux context: u:object_r:unlabeled:s0
I:addFile '/custom/etc' including root: 0
setting selinux context: u:object_r:unlabeled:s0
I:addFile '/custom/etc/filter.xml' including root: 0
setting selinux context: u:object_r:unlabeled:s0
I:addFile '/custom/etc/firmware' including root: 0
setting selinux context: u:object_r:unlabeled:s0
I:addFile '/custom/etc/firmware/catcher_filter_1_lwg_n.bin' including root: 0
setting selinux context: u:object_r:unlabeled:s0
I:addFile '/custom/etc/firmware/dsp_1_lwg_n.bin' including root: 0
setting selinux context: u:object_r:unlabeled:s0
I:addFile '/custom/etc/firmware/modem_1_lwg_n.img' including root: 0
setting selinux context: u:object_r:unlabeled:s0
I:addFile '/custom/etc/mddb' including root: 0
setting selinux context: u:object_r:unlabeled:s0
I:addFile '/custom/etc/mddb/BPLGUInfoCustomAppSrcP_MT6752_S00_MOLY_LR9_W1423_MD_LWTG_MP_V8_1_lwg_n' including root: 0
setting selinux context: u:object_r:unlabeled:s0
I:addFile '/custom/etc/mddb/DbgInfo_LR9.W1423.MD.LWTG.MP_NB6752_LWT_KK_MD1_MOLY_LR9_W1423_MD_LWTG_MP_V8_2014_10_22_13_40_1_lwg_n' including root: 0
setting selinux context: u:object_r:unlabeled:s0
I:addFile '/custom/etc/resources.xml' including root: 0
setting selinux context: u:object_r:unlabeled:s0
I:addFile '/custom/framework' including root: 0
setting selinux context: u:object_r:unlabeled:s0
I:addFile '/custom/framework/mediatek-op.jar' including root: 0
setting selinux context: u:object_r:unlabeled:s0
I:addFile '/custom/framework/mediatek-op.odex' including root: 0
setting selinux context: u:object_r:unlabeled:s0
I:Thread id 0 tarList done, 0 archives.
I:Thread ID 0 finished successfully.
I:InfoManager saving '/external_sd/TWRP/BACKUPS/p6000/custom2015-03-12--14-12-47/custom.info'
I:createTarFork() process ended with RC=0
I:Partition Backup time: 0
* Generating md5...
I:MD5 for /external_sd/TWRP/BACKUPS/p6000/custom2015-03-12--14-12-47/custom.ext4.win: 13ae7b343c95ea0663ec4e03387eaa95 custom.ext4.win

* MD5 Created.
Average backup rate for file systems: 45 MB/sec
Average backup rate for imaged drives: 0 MB/sec
[45 MB TOTAL BACKED UP]