Also, minute differences in the rod bolts diameters will place the rod caps in an ever so slightly different place than the old rod bolts. When you're talking about thousandths of an inch clearances, the least little change can be a big one.
The knurl on the bolt shoulder will open up the hole every time a new one is pressed in. The new one may not go exactly to the same position/centered as the last one, and now the rod cap will locate in a slightly different position.
Minor cases, the mis-match will cause a drag on the crank. I've also seen "more serious" cases where it will keep the crank from turning altogether.
Any time you change the bolts in a connecting rod, you should have the crank bore re-machined.