Aluminum heads and 63 vs 65cc chambers

By positive, do you mean below the deck? A +0.025" deck means the piston is below the deck 0.025". When the piston comes above the deck 0.005", it is -0.005" deck height. A bit confusing but that is the way it is.
How much do 340 pistons protrude above the deck in an unmolested engine?

In an “unmolested” 340 the spec is .018 POSITIVE deck clearance.

To actually get the compression ratio you might want the piston may have to be out of the deck 45-50 thou, maybe a bit more.