Then there is the native species. They had to avoid contact with them, so as to ensure they culture and social identity wasn't contaminated by Starfleet. How better to do that then by flying into their atmosphere only a few short kilometers away from one of their major temples, just to hide in the sea, then have to take off again and back into orbit, all without being seen! What?
IIRC, Scotty implied that the ship submerged out at sea and carefully moved up to shore underwater, over some period of time.