It will work fine if your deck height and head gasket choices give you the quench you desire. 0.035" is a bare minimum IMO.
However, the deck might not be square with the crank, and when you correct that you will lose some deck height. Also, depending on your head and cam choices you might wind up having to flycut the pistons to give adequate PV clearance. You also need to decide what fuel and compression you want to run, and figure in the deck height, piston cc, and head cc to get to the desired compression.
So, yes it can be made to work, but needs to be planned out carefully to avoid any unexpected consequences.
To me, a well planned build goes fuel>compression>head>cam>stroke>rod>piston.
jt