As long as the entire hatch is sheathed with mat and resin to finish then the filler is immaterial as it will be protected. Stain won't look good on resin so why not fair the surface and either gelcoat (with added wax) or paint. You can use car aerosols for a professional looking finish.
I generally just use Sika type sealants for sealing apertures. Makes a perfect water-tight joint as the sealant works its way all round and between the cables.
What makes it uncomfortable that you need to change?
The base look substantial so shouldn't be difficult to rework the whole seat using the base as the foundation.
In fact you could cut off all the upstands and make the base flat and then fit any suitable bench seat.
I have found “The Pink Stuff” spray is superb for removing mould on vinyl flooring used for cabin linings. It doesn't exude toxic fumes so presumably is quite benign. Well worth trying.
You may find a Seamastrr 30 in your budget with diesel engines. Huge accomodation and a reasonable sea boat, although displacement speed only. I know one that had twin 115hp Volvo petrols that topped out at 25 knots but I believe that was unique.
If you decide to go down the disengaging hinges route and can't find any I could make you a pair depending on the layout of the box and how it's sitting.