I think I found the problem. Apple defines pin #4 as chassis ground on Macs, but on an Apple IIgs it is defined for "3.5/5.25 Drive Select". Pin #9 is N/C on a Macintosh (some models provide power on this pin), while the IIgs defines it as "Drive 2 select". On the emulator schematics, pin 4 is grounded and pin 9 isn't connected to anything.

I have a feeling that this problem is related to why the 800k Macintosh 3.5" drive (M0131, the one without an eject button) doesn't work on a IIgs, but the 800k Apple 3.5" Drive (A9M0106 with eject button) does. I don't see any info in Apple IIgs docs on how Pin 4 is used to identify drive type. Pin 9 isn't used on Macs because they only support 2 total 3.5" drives in a given system.

Here is a summery of pin assignments from Apple regarding the IIgs are various Macintosh Models.

Apple IIgs: https://archive.org/stream/Apple_IIgs_Hardware_Reference#page/n87/mode/2up

Macintosh Plus and SE: https://archive.org/stream/apple-guide-macintosh-family-hardware/Apple_Guide_to_the_Macintosh_Family_Hardware_2e#page/n375/mode/2up

FDHD Equipped models: https://archive.org/stream/apple-guide-macintosh-family-hardware/Apple_Guide_to_the_Macintosh_Family_Hardware_2e#page/n387/mode/2up

Some additional info on other Apple II models: http://mirrors.apple2.org.za/ground.icaen.uiowa.edu/MiscInfo/Drives/pinouts.drives