The prevailing wisdom is that the studs may locate the caps in a slightly different spot thus throwing the line bore just slightly off.
I put main studs in my crate short block when I got it but didn't have it line honed. No problems after 10 years. I also installed ARP rod bolts in the conn. rods without having them resized. I'm not reccomending this mind you, I just didn't have time to have the machine work done.