I already checked the custom rules when I had DRC issues before (due to a syntax error). I’ve reviewed them again, and they don’t seem to be the cause here
I did not ask if you had once reviewed the rules (nor to post many screenshot). And cutting / pasting the text would have been both easier for you and for us compared to those screenshots.
What is the result if you go though the 7 steps I posted earlier?
(You can make a backup before you do this, just as extra security you don’t loose all your rules.)
Delete MPU.kicad_sch-bak (and others -bak) and zip will be smaller.
Yes, I thought that too, but I wanted to encourage Ryan to dive a bit deeper into his project and solve it himself instead of just letting us do all the work.
To me it looks clear where the problem is. The explanation can be found if you combine the generic explanation of the rule syntax in PCB Editor | 9.0 | English | Documentation | KiCad, and insideCourtyard().
EDIT: or actually just insideCourtyard().