It's true that the first release won't contain collision between water and construction elements... so for now water will only collide with terrain
However, this is definitely on our to-do-list
A dedicated water update is planned for the future which will improve the water visuals (it will add 3d waves etc), but it will also introduce collisions with construction elements. It will have some limitations though (for instance, water would not collide with very small or thin construction elements), but an underwater base will be definitely possible then (actually in creative mode it will already be possible to create an underwater base after the world update, but it requires the usage of static water, which will only be placeable in creative mode)
And will the regular water collide with static water?