Why is it you want it to be flush? That really complicates things. If you had your new cutting boards overlap the countertop you could use nearly any material you wanted and you could easily remove it to clean or resurface it. You could even have different inserts for different purposes, wood for cutting, granite for ? Umm, I don't know - just good looks maybe? Sealing it also would be easy with a gasket around the perimeter of the opening.

John