Well I asked, and the answer was - "It depends on the engine"... From what I can understand its best to try and replicate what came from the factory, the pistons came to the top of the block leaving the gasket thickness as squish clearance. There's going to be more squish area as the bigger bore pistons will see to that.
So... I put the block on the grinder

To get the whole thing flat - took 0.004" off the deck in total
Then the pistons and rods went back in

and the crown to deck heights measured - indicated by the numbers on the crowns.
These were then machined down on the lathe - a touch concerning because I was plunging a cutter into my new pistons.
While the pistons and rods were out, I checked the crank endfloat - 0.12mm which is pretty much spot on.
