I'm sure TOS is straight CP/M 68k (the commands are identical IIRC) and GEM the GUI just sits on top like MSDOS 6+WINDOWS 3.1. Kickstart and Workbench are not so cut and dry though, for example Windows doesn't use the same task scheduler or kernal as DOS it's pretty much a loader but doesn't Kickstart contain ALL the low level functionality of Amiga OS within the ROM e.g. time sliced round robin multitasking system AND what the BIOS on a PC does too?
Anyway the essential parts of Amiga's OS from 0.9 to 3.0 are basically bespoke versions of TriPos 68k (written by Dr Tim King of Metacomco at Cambridge University UK). Atari could quite easily have acquired TriPos for the ST range too. The Line A routines on GEM are god awful slow for graphical updates, they make Microsoft Windows source code look acceptable