Game Theory: Like the rest of the bosses, Bowser in Super Mario Sunshine is also a fake created by Bowser Jr's Magic Brush. After all, Bowser told Bowser Jr. to deal with Mario this time, so he's probably at home taking a break for the duration of the game. This also explains why his voice is weird.
The reason this goop Bowser doesn't dissolve in the hot tub is because the Japanese bath salts put into it (which are what make it green) prevent that. Either that or the hot tub water IS actually goop and not just the Gamecube not being able to make dynamic water.
WHAT IF the hot tub water that was dumped onto Delfino Plaza during the flood was from Bowser Jr. putting the goop Bowser in it, realizing his goop dad dissolved in it, getting rid of the actual water by dumping it, then making a tub of goop-water for his goop dad instead?
This started out as a joke but this is my headcanon now.