Depends on the cover
First - tether those covers! I did that before I ever hit the water with my Explorer. I’ve got a Valley day hatch cover on mine, which is stiffer than the NDK (actually made by Kayaksport). I use 303 inside and out, and it still fits very tightly.
I think it’s especially good to use 303 on Valley covers - they are made of sturdy stuff, but rot out a lot faster than NDK’s.
I also do the main hatch covers (NDK) inside and out, and have no problems. They go on and off easily, but there have been no surprises…
Alan