340 build

OK here is the math. you don't have to understand the math to use it!
.7854 X bore X bore(4.100 x 4.100) x stroke aka piston pop up(.018") = 0.2376463(cubic inch) X 16.387(converts it to CC)=3.8943099 or 3.89CC
So your piston sticking out of the hole as a flat top(no valve reliefs)=3.89 cc
Your Valve reliefs are 7.6 CC, Sooo, 3.89 CC (Minus) -7.6 valve relief CC equals a minus (-)3.70569 or 3.71 CC in the hole.

So when you use that calculator and it says (Input a positive number for valve reliefs.
Input a negative number if it has a dome. )
It has a .018" dome or pop up but it is actually in the hole 3.71 CC not 7.6 CC aka you us "positive number" on the calculator, not a negative number. Even though the math we just did cam up with a negative number.
compression is volume below piston (stroke)+ volume above piston, divided by volume above piston.
You add 3.71 cc to the head volume. if it had a dome that stuck into the combustion chamber, then there would be less space in the combustion chamber causing you to us a negative number.

If i lost you anywhere, let me know and i will try to explain better.
Note: I used the .018" pop up or above deck because what's what the piston manufacturer said it is.