I would venture to say that the motor in his truck has issues with the studs do to two issues.
Decking of the block and surfacing of the head. So, with the old style studs even if you take the webbing out of the covers, you may still have clearance issues.
The studs can be cut down using a lathe, the valve covers can be drilled and have small extension housings tigged on, you can drill the housing and put a breather over each stud, or you could replace the studs with the new style ones.
Before you go through any of that though. Do to the fact that the head on that truck has o-rings and was retorqued a few times. I would back off the nut, then check to make sure that the stud is fully inserted into the block.
I have seen where guys have backed off the nut while performing a re-torque and unknowingly backed out the stud as well. Then when they torqued down since the stud doesn't "screw" itself in, they end up with additional stud protrusion. Might check it out.