[Update] Fixed (for now). Not sure exactly what fixed this problem , so I'll list what I think might have fixed it.
1.) Most likely an update fixed the issue. I don't think there are patch notes for the scene editor so I can't know for sure, but that TaleWorlds fixed it themselves is most likely.
2.) Under the ''Shaded" dropdown menu on the main scene editor screen there are a few debug operations. I clicked through a few of them and after doing so, the test missions now properly render terrain layers. These should just indicate a problem, but maybe they fix problems too.
3.) I've gotten lucky somehow and tomorrow when I load the scene the problem will come back for unknown reasons.
Whatever fixed it I'm just glad that now I can run the test missions without my eyes bleeding. Here's proof that at least for me the bug is fixed: