What I would do is to use the positive deck height spec. with the valve relief specs and then do the same calculation with the piston down .500 with all the other specs remaining the same if you want to know the differences
The first calculation should be accurate
On your deal using the .500 down with no valve reliefs and then using your actual fill volume will tell you the actual dome volume with the valve reliefs
I use the .500 down method or what ever depth is needed for hemi pistons to get them below the deck to figure out their true dome volume is