It look like they haven't customized the icons and fonts yet (window's closer is also the same as on the PC-GEM).
PC-GEM has two icons sets: DESKHI.IMG and DESKLO.IMG. Atari decided to use only one icon set, my guess is that due to ROM size limitations: 192kB. I read somewhere that initially the plan was to use smaller ROM in the ST: 128KB.
Regarding CP/M and GEMDOS, below is a screenshot from Atari Corp. book before GEMDOS was born:
I heard that GEMDOS was initially a private project one of the DRI employee - Jason Loveman and was called "Jason DOS" / "Project Jason" and it was DOS 2.x based. Therefore history has come full circle: DRI CP/M --> SCP 86-DOS/QDOS --> MS DOS 1.x --> MS DOS 2.x --> DRI GEMDOS
Ok I've found that article: http://cd.textfiles.com/crawlycrypt1/program/books/progem/gemdos.15
There you can find GEMDOS vs DOS vs CP/M comparison:
https://docs.google.com/spreadsheets/d/12XHJ6YHRDfvNhtnlzEINBjRRXZPKvDQgI7AI424oTws/edit?usp=sharing