Unfortunately, I only did overworld stuff for ROTDS. I could probably learn how to create indoor maps as well, but anybody could arguably do just as good a job. It's a whole different ballgame because the indoor maps use multiple layers, and the tiles interact quite differently.
Because Ebot's Rock's rooms are mostly on the same map, and it's randomly chosen whether the rooms have passageways between them, you couldn't just take one of the rooms and make it watery. You could add in another map for 2.0 with some of Madsiur's expansions, and we could make a new room (or set of rooms) on that map.
Alternatively, we could make a clone of the original map. Then we could set the event code to have a 50% chance of sending the player to the flooded version of the map (which would presumably have the Serpent Trench palette and possibly a ripple effect), and a 50% chance of sending the player to the normal version of the map. I'm not sure if that would enhance the mazelike effect of the place, or come off as a lazy/transparent trick. It would certainly require less effort, and I don't think it would require applying expansions to duplicate a map (if you want to avoid that).
PowerPanda from FF6Hacking was working on the scenario changes. I liked his thought process on it, so I suspect the result is good, although I haven't tried it.