The version Atari bought from DR wasn't finished, Atari bought the source code and recompiled it for the 68000 adding support for their hardware (and GEMDOS). Apple saw the version DR bundled with the Apricots, and got all snotty about the trash can and movable windows, so for the next version, DR had to cripple a lot of the features of GEM. This didn't affect the version DR had already sold to Atari fortunately.
The version I have in my Apricot is very close to TOS 1.0 in many ways, but it's a little bit slow on a 4MHz 8086...