The bottom line is, the difference in this case is 6.5cc, depending on how you measured it, which is the .025 of deck.

To your point about the irregular piston shape affecting the value.....
The 4.50 x .025 area is 6.5cc.

If the fill down was done at .500 below tdc, the piston dish is 5.2cc.
If the fill down was done at .500 below the top of the block, there is a dome volume of -1.3cc.

The difference between the +5.2 and the -1.3 is still 6.5cc.

Think of it this way.......
Assuming this irregular shaped piston in a 4.50 bore is completely below the deck at tdc by .100(an arbitrary number).
Now slice .025 off the top of the block so the piston is .075 down the hole.
How much did you reduce the volume?
How much did the irregular shaped piston affect it?