If that part where the dome should be (the bottom of the piston when it's installed) is higher than the flat above the valve notches then yes, it needs to come out of the hole.
I never EVER deck the piss out of a head to get compression. One, it can be a flow killer. Two, it's a waste of heads. The engine is DESIGNED to have the piston positive out of the deck. That's the way it should be done.
You are running enough cam that I'd be damn sure (and the ONLY way to be damn sure is to measure the volume by doing the 1/2 inch downfill and then doing the math) I had at least a measured 11:1 and if you get to 11.25:1 I damn sure wouldn't worry about it.
