It never added up for me. I thought that taking deck to crank centerline measurement minus 1/2 stroke minus rod length minus piston hieght (center of pin to top of dome) would yield clearance, or amount piston is in the hole. My machinist said that one can't do that, just have to mock it up and take the measurement with a dial indicator.
I used 6" rods in block with line bore and deck squared (both shorten deck hieght) and I think that we ended up taking .012" off of the piston tops to get it .005 in the hole.
From the research that I did when dealing with it, it appears that stock we have about .035 clearance so your .005 should be fine, but should also be checked just like any buildup.
If you're getting the rods resized anyway, you might be able to get that .005 taken out if it is of concern.
Tom