I think that's a great idea and it is used by many other kayak manufacturers.
My wife made a similar cover out of an old nylon raincoat and bungee. Not as good as neoprene or rubber but still better than nothing.
It has definitely limited how much water gets in to our TI, though not eliminated it entirely. I suspect a little water gets under the cover when sailing at speed and punching through waves. Often there is a pool of water on top of the nylon cover when I remove the plastic hatch cover.
If you look at this post you will see other methods to improve hatch waterproofing, mostly involving seal replacements. Chekika reports his roids seal works.viewtopic.php?f=71&t=51372
BTW -You mention gaps around the hatch bungee screw in fittings (where the bungee's are anchored to the hull) but have you properly checked they aren't leaking? Pour a little water over each fitting and note if it is entering the hull. That is a common source of leaks as the thread cutting can be a bit hit/miss.
If it is, it's an easy fix -unscrew the fitting, coat the threads with sealant and refit. Any sealant should work as it doesn't have to stick to the PE hull, just fill the gaps. Both the fittings seen at the top of my pic above needed sealing.