Compression ratio shouldn't change on a flat head from surfacing if done correctly, decking the block will. When we did IDI heads, we removed the pre-cups, surfaced the head, then had a machine to surface the pre-cups. The pre-cups were re-installed and measured, then machined more if needed. The main reason being, a broach with a CNC cutting bit can, will and has caught the edge of a pre-cup in the machining process. The cups will sometimes move from the vibration of the cutter. This cutter is like a large flywheel, with a carbon puck that contacts and cuts the head, approximately 18" in diameter. It carries a lot of mass and has a lot of hp turning it, so if a pre-cup raises in it's bore ever so slightly, damage is going to result! There is also a protrusion measurement on the pre-cups. So, you surface the head, without the pre-cups, the cutout for the pre-cup now becomes less deep, so you have to remove material from the ledge it sits on, or the pre-cup itself. We could do both, generally you are only talking .002-.003 however much is taken off when the head is surfaced, and often times, the thickness of the pre-cups is still within protrusion specs, which might be the best of both worlds, no material removed from the pre-cups, but still within spec.
When doing a flat surfaced head, the valves are set deeper in the head (which happens anytime a valve job is done anyway), valve stems are cut to proper standing height on non lash adjustable valves, and the valves function just as they did prior to surfacing. CNC tooling is even available to remove material in the combustion chamber, around the valves to make the compression change minimal to non-existent. I've taken small block chevy heads and removed enough material from a closed chamber head to drop a point in compression when the customer needed lower compression (ie turbocharging or supercharging) in a class where stock heads must be used.
That being said, there is no doubt in my mind they pre-cups can be cut with CNC machining, seen it done. The question remains who has an o-ring gasket, and it sounds like several places might be taking on that task.
. I've heard lately that 7.3 heads should work on a 6.9. If its possible i may just give these a shot with my head studs 
. Would the heads be able to wiggle around with the difference, or is there something that would hold them in place laterally? I wonder if they can open the coolant ports too
A member had some water issues in his rebuild. Seems water was flowing up the head bolts into the heads... His original thoughts were the head bolt holes drilled and tapped in the block entered the water passages like many gasser engine do. So he removed the heads to find no such issues. I even checked this out on my block... None of the drilled and threaded bores for the bolts go thru to the coolant side of the engine. So after looking closely at the water travel path he found it was the precup in the head. It was found to be too high and was keeping the gasket from covering all the head. It was only .0035 above the block but it was enough to leak. So make sure your precups are no more than .0025 above the deck. I would personally kep them no more than .0001 or even with the deck...
