That's the editing because they put the Starfleet scene right after the Vulcan Master tells that to Spock.
The powerful tonal contrast, between the aridity of Vulcan, and the pristine, near-palatial beauty of Starfleet Headquarters on a paradisaical Earth, certainly gives that transition a lot of clout. The sudden gear switch in Jerry Goldsmith's score is also very satisfying. The former sequence with Spock has a beautifully austere and remorseless air, while the San Fran sequence is bustling with optimism and life. The visuals and the music really sell that evocative contrast.
Moreover, the Spock sequence is essentially a teaser (along with the Klingon battle sequence that opens the film), before the "main course" of the first act, which is concerned with Kirk and his crew readying the Enterprise and reaching the mysterious intruder. This enables the Spock sequence to inflect the film with a good deal of metaphysical melodrama -- we see V'Ger attacking (or defending itself -- the difference is hard to perceive) in the opening scene, and we then get a mystical revelation that this "thing" is really a "consciousness in space", and that Spock, Mister Logic himself, has some sort of
connection to it.
Ergo, a certain measure of tension is introduced into the film, which builds up the idea that the technocratic confidence of Starfleet won't be enough to deal with this threat -- Spock's immersion in Vulcan mysticism (and his gradual relinquishing of its manacle-like hold on his mind) will be an essential component in unravelling the mystery of V'Ger, and in neutralising the existential menace bearing down on the Federation.
It's rather fetching that we don't see Spock again for a while after his short introduction on Vulcan. And his substitute is killed in a transporter accident, heightening the feel of his absence. We're frankly waiting for Spock to appear and begin to set the Enterprise and her captain right. It isn't really "the Enterprise" or Star Trek until Spock arrives. I love the thematic intensity of that idea.
One oddity of the Vulcan sequence is that the Vulcan High Priestess very casually describes the imminent threat of the cloud and seems to already know what it is (at least as well as the Federation at that point), without showing the faintest concern for its starship-chomping abilities, or the fact that the Federation is at urgent risk. Yes, they're Vulcans, and apparently fairly aloof Vulcans at that, but this aspect also adds to the strangeness of the scene and the movie. Do they already know about V'Ger? Do they see it as a passing danger? Are they already indifferent to the material fate of the Federation, of Earth and of Vulcan, and of their very lives and the lives of others? If everyone returns to The Source via digital patterning (remember: Spock describes V'Ger as emanating "thought patterns of exactingly perfect order"), so be it?