I think I found the solution to the "help I'm stuck in the basement" bug. The pushable boxes' textures don't render, but the collisions do. If this happens to you, most of the time you can just interact with the boxes to push them and get out or get to the cook.
Edit: turns out you can't push the invisible boxes, so the solution I found is to always solve the box puzzle when you see it unsolved and hope for the best.