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That gap caused by the grate would almost act like a gap left with an under gravel filter. It will create "deadwater" movement areas.
Also you say you used epoxy to seal it...did you "seal" the back side and bottoms of the pieces also???
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The bits sit flush to the glass so there is no gap really.
This pic is not great but you can see that behind the rock there is a big gap where water/fish can flow.
This rather simplistic cross section shows how little foam is used relative to the rock and how open the rear is - as a vertical cross section it doesnt show all the holes and gaps that link the front and rear allowing water and fish back there. As the crate is full of holes there is no "trapped" dead spot any more than there would be if you just stuck a sheet of the crate to any tank wall.
In fact, notice how at the base there is LESS space for food and muck to get trapped!
As for epoxy - i only covered areas that i thought UV would get to and might be visible (as the visible areas extended to places UV would never get this was the primary focus)
This leaves the rear and underneath of some bits of foam uncovered.....i dont believe that's an issue as i believe it will only corroded if exposed to UV light.