This is my first post here.
I've been following the project with interest after Mr TerribleFire mentioned it on his live streams.
I have a small retro collection, including a 2600, 130XE, Jaguar etc., but don't actually have an Atari ST right now. (I know, I know. hehe)
I loved using both the Atari ST and "the other one" in the 90s and beyond. I thought this project was neat, and might inspire me to get hold of another ST.
I wondered if I could help at all with the diag / PCB stuff?
@exxos - Are you intending to release the PCB files eventually (or have already), or will it be closed-source for now?
Either is fine, obviously, I was also just wondering if you are planning to manually route the PCB as well, or just use the autorouter?
tbh, I think the clock frequencies involved are just edging towards the point where manually routing the busses may help with reliability.
If it's only around 32 MHz max, then I guess it's not that fast really, but I haven't used any autorouters in about 10 years, so I'm happy to help if I can.

(I recently did a re-design of the Nintendo 64 and Dreamcast motherboards, and those were both manually routed, albeit with the help of the "Interactive Routing" on Altium.)
I also think this project could be a good opportunity to look into doing some CPLD replacements for certain chips, maybe just for the rarer ones?
And, I reckon you could get some VERY valuable diagnostic info by hooking up various chips on the board to an FPGA dev board.
I've done something similar for CPUs, and things like Roland synth chips.
For things like RAM, you can actually get the FPGA to display chunks of memory in realtime to a VGA output. This is what I did for the synth chip...
If you hook it up to a CPU, you can trace the memory fetches etc.
Obviously it would be nice to have a proper Logic Analyser like TF has, but you don't need anything too fancy to hook up an FPGA board to a CPU, just some IC test clips.
I've been using a Terasic DE1 board for around ten years now, and I've been able to connect it directly to "5 Volt" systems without ever zapping an IO pin. It technically doesn't have "proper" voltage translation on the board, just some 47 Ohm resistors on every GPIO port pin, but that seems to work great.
DiagROM is great, too, but testing the chips directly could be useful for times when the board isn't booting far enough to run the ROM properly.
You can very quickly write some Verilog for other custom chips, too (assuming you can clip onto the PLCC chips easily).
Just throwing a few ideas out there.

P.S. I go by "ElectronAsh" on Twitter etc., but usually OzOnE on forums.