I agree that the inability to live under water in a flooded world is an obvious flaw. And I don't really understand why spend so much effort on interplanetary trading, on tokens, when basic things like the above, or visual bugs, or penetration through rocks have not been fixed yet.

Well, let's say the developers do not want to add mandatory gateways due to the fact that the astronaut is in a spacesuit during the entire time he is on the planet during its terraforming. He does not take a shower, relieves himself directly in it, does not get sick and does not need sleep. (It seems that this is not a man, but a robot. It is not clear then why he needs air, water and drink?) After all, the game is a casual farm, not a sci-fi survival simulator. But the issue of tightness of modules is a matter of common sense. What prevents us from excluding the installation of a hermetic door in a module partially or completely submerged in water, but allowing penetration into this module from above, through a closely adjacent module? Will it destroy the fundamental concept of the lore of the game, or will it create contradictions in the logic of the system of the created world? Hardly.

The base modules aren't gas proof (air tight). They maintain the same air pressure and oxygen concentration as the outside. Your oxygen refills while inside but the drop pod also does this with one of the sides being open and also floods.