Most common issue when using studs is that studs will touch inside of cap and prevent proper setting of #3 cap for correct end play--factory bolts 'hang' in the holes and don't touch cap--so..answer is just drill holes in #3 cap out a tad --do that and usually studs will do fine but..we ALWAYS brush through when using studs and make it just right.
Boring is done when caps are changed--
Rollmaster and others offer sets that are .005 shorter when needed
I agree when you have to bore one it can be tricky and cause all kinds of trouble if not done correctly--
It is also rare when bolts will not hold what you are doing--studs make folks feel better but are a PIA back at the seal holder, with the thrust issue , and really may make you sleep better but I can't prove they are any better or that they prevent anything! Timing errors that cause detonation is what makes caps 'walk" and no stud will prevent that or make it better IMO
We do it because customers request it not because we think it is any better