Should Naval units be able to use a water based stargate? I think so. It would make it possible to invade water planets with little land mass.
Yes. Naval needs all the help it can get currently. A unit blob of naval won't take over a planet in 3 seconds. Water worlds will be something that could happen where a ground based teleporter wouldn't work. and giving current air the power to swap planets is too much due to their rapidness. I would also argue for a late game orbital teleporter to help speed up planet swapping and invading in general. Question is what fabber can an Astraeus pick up and drop off in water beside the commander? Otherwise to build the initial teleporter you'll need orbital fabbers.
Id love it to be a submarine gate instead of a ship gate, just for the added stealth and infiltration possibilitys.