Pics!? Without seeing it, I'm thinking you probably need to pull out the lid assembly and re-install it, possibly shortening the standoffs that are causing the gap.
In any case, I'd use the lid trim to fill the gap, and not some filler material.
I mentioned tuff seal it's called tuff-coat!! The spray in liner .but you are correct on the gap. I hate your solution lolol because that's what I was thinking my options were going to be thanks.
Everything is fiberglass . I did find a better way of removing the old hard marine carpet glue!
after working with acetone with very little success .And that old fashion easy off oven cleaner. Spray on let set for about an hour use a puddy knife come right off. Wash down and you done .
Dont know if there’s room, you know the welt cord that your seats have car boat whatever. Piece of vinyl sewn over a thin cord. If your doors are thick enough to glue or staple a welt cord in you could have someone sew up pieces for this pretty cheap. Pick out some vinyl that matches your colors. The cord could be whatever thickness you need to fill the gaps, I would have it sewn at the cord and the edge to hold the flaps together.