Graham
Not being the proud owner of a hole in the bottom of my boat (filled, part time only, by an outboard), I can only generalise. There are now widely available (e.g. see Amazon) 'cyanoacrylate activators' which, used with superglue, enable almost everything to be glued to almost everything else. And they work. Last year I wrote up (somewhere else in the forum) using one of the first available in the UK, which actually came from Poland, to stick thin PTFE sheet to polypropylene webbing - two of the most previously no-no substances you could think of for gluing together purposes. A year on, they remain firmly fused to each other, and look to be inseparable for the long term, bless them. A few weeks ago I used 'Xpert Activator' + superglue to stick rather thicker PTFE sheet to two-pot-painted surfaces when re-assembling my repainted kick-up rudder: again, perfect result, and a rolls-royce smoothness as the rudder blade swings up and down.
Using this new glue technology, I was wondering whether you could find some sort of pliable plastic sheet to stick round the edge of your cover, slightly over-filling the hole and bending upwards round the edges, to keep most of the splash below the cover. The right degree of bendability would be critical. It might work even better if you reduced the size of the infill to leave a deliberate gap, now filled with your flap-valve material and even with a plastic edging strip along the free edge to improve the seal. The point is that you can now stick almost anything to anything else.
Just a thought, hope it helps. I think 'gluing' has been quietly revolutionised, and the possibilities are endless.
Michael R