RPM Airgap

Hogging out the bolt holes is a normal thing to do when fitment is tight. Chances are that the intake is made/cast slightly different from the Holley is possible as well as a possible engine block decking, head milling, intake milling, and gasket thickness all come into play.

Pushrod length on a Hyd. rocker can pretty much still use a stock length on a stock engine with a stock unmilled deck to a very well milled deck. And again, gasket thickness changes help/hurt this.
There is some area here that is forgiving. But as said above, as long as the rocker geomentry is t bad, your good to go.