That's because early pistons have a lower wrist pin location (due to a shorter rod) and later models use a longer rod (with higher pin location in the piston). Combine an early piston with a late rod, and you have the piston crown way above the deck.
Combine a late piston with an early rod and you have a 4:1 compression ratio (possibly an exaggeration as I've not done the math to confirm this).
I like the late models as they're better for high revs, although the wrist pin location can still easily be moved up .1 to .2", and a longer rod used to improve high rev stability further, and decrease cylinder wall loads. Torque will suffer a little bit, but it's not that severe since the CVH is already a very long stroke design.