And actually the Enterprise never ever landed in other films because it was not designed to ever land, and would break apart on entering an atmosphere?
"Tomorrow is Yesterday". The Enterprise is identified as a UFO against blue sky.
Where, however, it only spends a brief amount of time. Generally speaking, you would nevertheless agree that long spells in atmosphere = bad for starships the size of the Enterprise, right? (Voyager in fact made a specific point about this by giving its starship the then-never-before-seen ability to land in atmospheres.)
In fact, the creators agree. Hence the thrilling sequence at the end of STID where the Enterprise is about to break up on reentry if Kirk doesn't save it. Which, I know this is gauche but still, some might say was perhaps slightly inconsistent with the ship being able to hide on the bottom of oceans.