Speaking as someone who regularly works a variety of boats across the L&L I think you are over thinking this.
If your stern doors are so poorly sealed you need tape, fix the seals. If your engine board drains are blocked, clear them.
If your welldeck scuppers (drain holes) are too small, make them bigger.
@dmr suggested that a cruiser stern might be better than a trad for working locks he freely admits he hasn't done as his boat is too long. I disagree having done them dozens if not hundreds of times. Standing on the step with the doors shut behind you is by far the best way to cope with some of the leaky gates!
You can do it with a cruiser stern and good waterproofs, but I prefer it my way.
The crucial point is that if you are in danger of swamping the boat while working a lock, you are working the lock wrong.
Henhurst lock at Wigan currently has both ground paddles out of action and no baffles on the gate paddles, so working it requires a delicate touch on the windlass. It can still be worked safely but needs a bit of care to do so.