As far as the screw actually screwing into the body, it's hard to explain, but simple in concept. You won't find a single quality bolt-on body that allows for the screw to to not just pass through. You want to remove that from the equation and have the purpose of the screws to attach the neck to the body. The head of the screw and neck plate act as the anchor. That is all you want on the body part. You don't need the screw to actually screw into the body, because, A: The anchor is doing all the work it needs to do there. and, B: Unless you have the neck super tight against the body when you screw it in (and even if you do),
you are basically just screwing the neck plate to the body and not getting that perfect connection to the neck. If you remove the actually body from the screw equation, then you are getting 100% just body to neck attachment.
God i hope that makes sense. I'm not great at explain things like that, but it's basic physics.
Edit: Some Fender models do not allow for the pass through of the screw. It's a common mod to drill them out so they will pass through for a better grip on the neck. However... this shows how much of a big deal this isn't. I definitely have my opinion on the matter on about it SHOULD be done, but in the end, it's not gonna make a HUGE difference. I'm a man of simplicity though. Fact is, you'll get more force on the neck/body connection if you allow the screw to pass through, so why not do it that way?
https://www.callahamguitars.com/tech_yo ... kholes.htm