The "problem" with this example is...... The pistons stick out .025".

If you move the piston .500" from that position it's only down .475" from the top of the block.

So, you're going to seal up the piston to the bore, put your piece of plexiglass on top of the block and fill it up.
The OP said they observed 129cc of volume to fill it up.
The piston isn't .500" from the top of the block, it's only .475" from the top of the block(if it's .500" from tdc).
The area for the 4.5" x .475" bore is 123.8...... Not 130.3.
So if you observe 129cc fill volume, you have 5.2cc(+)worth of valve pocket, not 1.3cc(-)worth of dome volume.

You've poured 129cc of liquid into what should only be a 123.8cc hole.

That would give you the 1299.5/94.5 = 13.75 result.

1205 - swept
76 - gasket
19.8 - gasket
5.2 - dish vol
-6.5 - deck
------------
1299.5
94.5 total minus swept
-----------
13.75(1299.5/94.5)


In this case, whether the .500" dimension is from tdc or from the top of the block changes the results by almost 1 point.

It looks like this is a case where a slight difference in how some terminology is interpreted makes a difference in the bottom line.

I use the fill down volume to determine the piston dish/dome volume by itself.

The OP would have to clarify how they did it to know what the cr actually is.