[Moto G4 Plus Guides, News, & Discussion] echo92:
1)The opening post does not cover the act of downgrading a stock ROM, that's correct. Rather, it only appears to cover flashing back to the same build you had when you rooted (i.e. re-flashing the same stock ROM build, or rather the parts that get modified by TWRP and rooting), as mandated by this warning in the opening post:

As the message stipulates you need the same build number, you do not have to flash the bootloader if you don't wish to, as there should have been no changes to the bootloader/GPT/modem caused by rooting (only stock firmware/OTAs can touch this level of firmware). Since you're flashing the same build and only restoring the partitions touched by TWRP and root, the bootloader should be and stay on the same patch level. You can flash it if you want to, though you'd be re-flashing the same bootloader. Flashing the bootloader is only critical if you're flashing a newer build than what you had.

2)You cannot downgrade the bootloader in most if not all cases by flashing older device firmware, especially with the newer (B1:05 and above) bootloaders. Attempts to do so are generally blocked by your device bootloader as a security downgrade/pre-flash validation error. Furthermore, as you have the NPJ25.93-14.5 build, you also should have the B1:06 bootloader. B1:05 bootloaders and above appear to be a cause of hardbricks, perhaps because the bootloaders are sufficiently different to older bootloaders that, if overwritten by old OTA updates, they will fail the upstream verification boot checks and cause a hard brick. Also, B1:06 had a bootloader vulnerability patch, so it could well be Motorola blocks downgrades to stop users from re-opening the bootloader vulnerability. In my view, it's not a good idea to downgrade or mess with the core part of the firmware that permits your entire device to boot anyway...

3)You could follow this guide and flash bootloader, only if you're flashing the same build of stock ROM however for the reasons mentioned above. I understand your reluctance for flashing NPJ25.93-14.5 as we can't fully verify the integrity of this stock ROM and you'd like to maintain as little untrusted software, I've not seen any malicious reports for the stock ROM builds from the Motorola Firmware Team however: https://androidfilehost.com/?a=show&w=files&flid=72578

I'd suggest downloading the NPJ25.93-14.5 stock ROM, then following the flashing instructions as described in the opening post to revert the rooting changes. Afterwards, you should receive and be able to install a Motorola OTA, which may go some way to verifying the stock ROM's authenticity (else an unofficial or altered/manipulated stock ROM would likely fail the OTA update).

Instead of the opening post flashing instructions, I'd suggest the following commands (to cover flashing /oem and erasing cache - you can always append the bootloader flashing command to the beginning as well)

fastboot flash logo logo.bin
fastboot flash boot boot.img
fastboot flash recovery recovery.img
fastboot flash dsp adspso.bin
fastboot flash oem oem.img
fastboot flash system system.img_sparsechunk.0
fastboot flash system system.img_sparsechunk.1
fastboot flash system system.img_sparsechunk.2
fastboot flash system system.img_sparsechunk.3
fastboot flash system system.img_sparsechunk.4
fastboot flash system system.img_sparsechunk.5
fastboot flash system system.img_sparsechunk.6
fastboot flash system system.img_sparsechunk.7
fastboot erase cache
fastboot reboot

However, I would strongly caution against downgrading your stock Motorola ROM, or if you do downgrade, do not use/install OTA updates. I should also note this behaviour is not unique to Moto G4 devices, other Motorola devices have the same restrictions, and I imagine a lot of other manufacturers do not envisage users downgrading their stock firmware.

Custom ROMs, by their nature, do not affect the bootloader (and should not have any means to either), usually only the system partition, so you should be safer with custom ROMs in regards to flashing. I'd suggest reading up on custom ROMs that attract you to be aware of bugs/limitations - generally, they are good though. Also, with a custom ROM, they appear to only apply security patches in the system/user space, any underlying security issues in the device firmware itself would only likely be resolvable by Motorola patches/updates.