I have head 'studs' on my engine (427 side oiler). I removed a couple of studs to swap out the heads with the engine in the car. Not a big deal though. But I wouldn't use studs 'just' to make sure the head gasket gets lined up, not worth the effort and actually, it's pretty hard to 'screw up' the head gasket installation. You should have to 'dowel' alignment pins that match holes in the heads and blocks all ready for 'alignment'. If not, why not? Where are they?
My block used studs because it used to be running 12.5 to 1 and turning 7000 plus rpm. Craked the heads during torque down? Whew, the more I hear about alloy heads the less I like them.
iron heads here...