With no mods installed, after setup when the game reboots, it appears to be vanilla, and then launching the game again says it's modded but it's a black screen

I've never made a github issue before so I don't really know how to format these
I am attempting to mod a game made in Godot 4.5
This same issue occurs on 4.x-dev and 4.5 and a bunch of things
It reboots, is in a vanilla state, so I relaunch it and it is just a black screen.
NO MODS installed btw

Yeah