That screw is probably 0.1mm shorter specifically so the traces can be routed under it. ... When you have defined size and weight, you make a lot of otherwise odd decisions.
This was my initial thought, too. It certainly
could have been intentional, but that would require conspiracy between the board designer(s) and the case designer(s), and probably a few other folks too. Much more likely, the odd screw length was chosen as an easy way to solve the problem of having too little clearance with their first choice in fasteners. Could've even been a design error, and just no reason to rectify it with a new board or case when a different screw would button it up nicely.
But this is the most convincing argument:
I don't see any intention from Apple to prevent their devices being repaired.
There are a lot of tricks they
could have played to make life difficult for aftermarket service techs. So I'm skeptical they left the front door unlocked, but stuck a bucket of ice water on the door frame in case anyone tried to enter.