I am planning on putting the hatch covers in their recesses and glassing the whole deck at the same time.When I get around to it cut the glass and install the gaskets and shock cord hold-downs.

I think there is a 'Law of Epoxy': "If you want a strong bond, you need to do it right, but if you let the slightest bit of epoxy accidentally get where you don't want it, the bond is permanent!"
Glassing the hatch covers and deck 'together' (perhaps I've misunderstood your plan?) seems a bit risky to me.

If I were making wood hatch covers, I'd try to get the glass wrapped around the edge.