What is the proper way to check piston to deck height with taking piston rock into consideration? Measure the center of the piston and give a few thousandths extra? Or do you rock the piston "up" and take a measurement (X), rock the piston "down" take another measurement (Y), and then Add x+y/2?

You can do it like that or get an approximate clearance for piston to wall and use brass feeler gauges between the piston and bore.

Example - .004" piston to wall - insert a .002" feeler gauge on each skirt then get it to TDC.
Takes the guesswork out of it.

That works if you want to get under it.
If you can't, the distance between the side of the dome and the wall from the top is much larger, perhaps .015" each side.

I will defer to others (especially Cab) for the final word but I would rock it on each side & see what you get for deck clearance with the piston "up" on each side at that point cuz that is what is potentially going to be the critical "contact" area when it's running.

I use a dial indictor on the outer most edge of the piston on the cam side and use a narrow thin screw driver blade on the motor mount between the piston top and cylinder wall to rock the piston over to get the low side measurement on that side, then reverse the piston to rock towards the motor mount side to get the high side. Do the same on the motor mount side to get the highest reading on both side of the piston tops and use a minimum of .035 piston to head on steel rod motors, more clearance for aluminum rods per the rod makers suggestions

You should be measuring inline with the wrist pin, rock will be greatly diminished.

True that if you want that measurement, if you use that measurement what happens to the edges of the pistons when rocking up and down on both sides
The closet part of the piston is what will hit if it is to close