Kickstart 45.057 (AmigaOS 3.9) vs Kickstart 45.061 (Amiga Forever 2016)
Workbench.library was removed in all versions of kickstart 45.061 which gives it less flexibility as a system with the issues all A4000T have had since 3.1 for having the same "feature".
Format of comparison: Kickstart 45.057 / Kickstart 45.061 / Comments
exec 45.20 / 45.21 / V45.21 has the RomFixes & SpeedRom patches applied to V45.20. It seems to introduce a new bug (1)
scsi 43.43 / 43.46 / V43.46 has the LBA48 support fixed
filesystem 45.13 / 45.16 / V45.16 contains bugfixes done to V45.13
expansion.library 40.2 / 40.3 / V40.3 contains a bugfix to properly handle some ram expansions
Note (1): It is yet to be confirmed officialy, but some users have reported floppy issues. I have been told that the matter is currently being investigated.
So basically, they are not the same, although they share common ground, and both of them donīt contain the latest modules available, and I am not talking only about hacks, but also some work that the former Amiga Inc. developers have done to bugfix and enhance them. BoingBag 3&4 contains these newer modules, and of course, some other stuff too.
And then here, I am just mentioning kickstart differences. Disk based differences from AmigaOS 3.9 and Amiga Forever 2016 3.x are also quite relevant.
So the point Minuous made, still stands.