Considering the cliff and all, it's apparently possible to fly a starship into that location and out of it without being spotted by the natives in their village or its usual environs. That's probably what the shuttle did, too - looping around the mountain and coming in under the horizon. I mean, if such a safe approach route did not exist, how did the ship get there in the first place? It's just that there was no time for the safe route when Spock was about to fry, and the natives were right next to the ship anyway.
Was the underwater parking slot supposed to be a long-term base of operations? Things speaking for a mission that only lasted for a few hours, total:
- Scotty still hasn't come to terms with being underwater
- The plan to evacuate the village is half-baked but clearly extremely time-critical
- Kirk doesn't know that the beast is part of the plan
- The shuttle flight and the evacuation take place in synch, while there is no obvious reason for such synch other than both requiring great hurry
Things suggesting there was some preceding activity before the cameras joined the action:
- Spock has created this device that meets the needs of the day; it's not as if those would be standard issue (or else an expert of Spock's caliber wouldn't be needed for inserting the device)
- Well, not much else...
Yet the heroes have gone to the trouble of taking the ship down, presumably during the previous night (as the location, while below the horizon, isn't all that far from the village). We could plead a combination: the heroes arrived in orbit, spent a realistic time spotting and analyzing the upcoming big kaboom, spent a realistic time devising a countermeasure, and then landed to execute their plan. Possibly the plan included the option of taking all the natives aboard the ship if everything else failed, and that couldn't be done by transporter (too slow) or shuttle (natives putting up resistance, and too slow), but might be done by ushering everybody in through the shuttlebay doors in one great panicky rush!
Timo Saloniemi