Your ideas seem good, particularly when backed by your experience.
I am think of setting up our new windlass to control only with your keyfob idea, but with manual switches inside the forward cabin (hence out of the weather) in case of radio failure. In our layout, such switches would be usable by reaching through a hatch, but not convenient, and certainly not for routine use.
Like you, I would have a spare keyfob, or two.
I like avoiding making holes in the deck for switches, and also keeping all switches out of the weather. the windlass itself will be in the anchor locker, below a hatch when not in use. This location is of course still damp due to condensation etc, but protected form salt spray.
The control box, relay etc would be in the forward cabin.

I also visualise a manual breaker to cut power to the windlass inside the forward cabin. This would energise the windlass controls only when windlass use is intended.

Comments form those with experience would be welcome