The milking parlour stool is a very good example of what you're trying to say. Three legs good, four legs bad.
This is a sound engineering principle but it does not apply to this situation. An accurately cut neck pocket made for a the neck root giving you a push fit is what makes the joint strong. The screws are only there to keep the mating surfaces in close contact. If there are lumps in the woodwork, there is something very wrong. If a shim job is badly executed it can compromise the contact surface area too.
In those cases, no number of screws or bolts (even using thread inserts) will help. You can't polish a turd. You can't make a silk purse from a sow's ear.
Again, three legs good, four legs bad. It works for objects that need stability on uneven surfaces but it does not carry across to the neck joint.
What makes the neck joint work is the large surface area where the two pieces meet. The screws (bolts if you like) simply hold the two pieces in contact.