You would have to adapt the existing connectors to something PROC boards could accept. I'd suggest not chopping off the connectors in case at some point you or a new owner wants to convert it back to the original boardset.

Atari doesn't have a lamp or switch matrix, so you're good there (P3 doesn't support a switch matrix).

I'm not sure if the software would be able to handle the digit displays or not. Out of the box, I think you might be limited to an LCD with P3. I remember seeing some 3rd party work on digit and alphanumeric displays, though.

https://pinballmakers.com/wiki/index.php?title=Main_Page

I just remembered that there were blank PCBs on ebay for a while.

edit: sounds like Houston pinball made them. https://pinside.com/pinball/forum/topic/what-s-the-deal-with-this-newly-assembled-atari-mpu#post-5376152