After a lot of tinkering, I just figured it out (kind of). It will only execute the PHP script if it is on the index of the subdirectory and if you try to go to the subdirectory (apps/ServerStatus/ works but apps/ServerStatus/index.php doesn't). It works if you go to any PHP script on the server root. It also executes any file is it is executed with JavaScript.
So the new question is, how do I make it so it executes files in a subdirectory if it isn't named index.php, too?
What says "validation failed" and what it it validating?
You definitely have something very wrong.
Perhaps you should start again with a vanilla reflash.
Javascript is run by your browser and has nothing to do with php.
I know, but it can tell the machine to execute the PHP script, which is what I'm doing. Anyway, this is solved now. It seems the issue is less with configs than it was with my lack of knowledge of how HTTP servers worked.
Glad you figured it out - I guess there was nothing actually much wrong with your config. Jumping in and trying is a good way to learn 
If it is now working for you, you can mark the topic as solved:
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