I think you've missed the point of what a "long take" is; ultimately its charm/value lies in the fact that it's a meat-world, real-time thing. Collaborative groups -- the film's director and ADs, cinematographer and assts, lighting director and assts, set designers and assts, scriptwriters, actors, and myriad workers -- all have to coordinate exquisitely to push beyond their normal boundaries of time (and usually of space). In one regard that work is similar to the coordination needed to efficiently produce a CGI sequence, but the big difference is that, as you noted, when the mountain isn't quite in the right place/shape, the CGI-er can "back up a few frames" and grow a notch in the mountain. In a meat-world long take where the mountain is out of place/shape, you have to reset the whole scene. There's some "making of" dox about the OK Go "This Too Shall Pass" viddy that illustrate this very well.
Missing from TFA are two of the most landmark uses of long takes in modern cinema: Hitchcock's Rope and Welles' The Magnificent Ambersons. Rope -- which is nothing but long takes, 10 IIRC -- stresses the actors: each shot was basically as long as the film in the camera magazine (10 minutes), forcing the actors to summon their best "stage play" skills while still accommodating cinematic conventions. The Ambersons' most noteworthy long take, the ballroom scene, stresses the various directors and crew with an extended backtracking shot through four rooms of the Amberson mansion (following the action through a set of French doors was considered a technical tour de force in its day).
And, of course, there's the matter af art. The Genesis sequence in Khan is hardly art; it portrays nothing that couldn't be replaced by a few seconds of explication (indeed, I would say that in its context that CGI sequence is merely the 23nd century equivalent of a PowerPoint presentation), does little to drive the story forward, and carries no emotional impact (unless your emotions are driven by your CGI-detecting circuits
What do an extended CGI sequence and parking lot surveillance footage have in common? Neither qualifies as a "long take".