Done it both ways. I have even used alluminum spacers on top of the plate and the original head studs to simulate the heads best I could. I don't know any practical way to do it because you need to stroke through the end of the cylinder but buttoms up with the head bolted on would be great IMO. But, no physical way to do it that I know of.

My opinion a block run at a certain bore for a season. Then bore over .005" new pistons and then do all the tricks you can when finish honing. Even bolt the heads to the block when final sizing the guides and lap the valves. OOOOPS did I give something away.

I let an engine get away that the block was done by Diamond for the Pro stock truck exhibition. They seasoned the block with a vibration process they do after every machining process. But, this was done on Mopars nickel. They never used these three blocks. But, it was a great one for me.

Leon