I'm guessing that every piece of their kit and manufacturing capacity is custom made to order. The difference between making their custom screws use one shape of head vs. another is probably negligible in terms of cost to them.

Yes, you said that already, and even though you haven't provided a shred of evidence I'll let it go, because even then there still must be a payoff for them to do it. Someone went to the engineers and said "Do this differently," and they didn't do it for laughs.

I was making my implications explicit. I'm saying that your original thesis that manufacturing cost was a significant deterrent to doing it differently was wrong, because they're never going to use regular screws, they're going to make them custom to fit the case, so making them with a different head is not an issue of manufacturing cost at all. But sure, there must be some reasoning behind their decision, most things they do are deliberate. If there's nothing user-serviceable, then they probably save money from people trying to open their computers up, screwing them up, and then trying to pass off the problems as manufacturing defects. I don't see anything nefarious in that - their user upgradeable computers are really pleasant to get into.