Re the walkway formation, they probably would have just used the same moire slot gags they used elsewhere in the V'ger finale to show the paths assembling. Yeah, shooting animation on twos was just dumb, and shows a lack of understanding of what they were working on. They confused the standard for cartoon animation with VFX animation, the latter almost invariably being shot on ones.
The Earth DOES look off in the DE. They probably used photos of the Earth rather than original artwork as was used back in 1979. I've got photos of the artwork of the Earth from when V'ger goes poof, and it's a flat down-looking painting of islands on water that was projected onto a hemisphere painted white. (A separate transparency of clouds was photographed the same way.) Et voila...
The drydock scene always suffered because they spend too much time circling around the outside at first teasing, but showing too much. By the time we get the big reveal, it's not such a big deal. Most of the shots even afterwards are typically 23% too long.
As to San Francisco, it's another case where the DE team either didn't do their homework or changed stuff against the original intent. This is the tram station as designed, and that's San Francisco as designed. Smaller city, more green, lower profile, perhaps inspired from the murals of Arthur F. Mathews, and rather
Paolo Soleri-esque, the only recognizable structures being Coit Tower and the Transamerica Pyramid. The station exterior here illustrates
why the interior wall is shaped like it is: the one reflects the other. No room for TOS shuttle platforms,
as designed. The city and the station match what's seen in the long shot past the bridge that did make it into the film. The SF of the DE isn't anything like what Gene wanted; it's what the effects artists wanted, retconning it to fit with the later movies and their own tastes ("A shot Mike Okuda and I put together for Star Trek: TMP – The Director’s Cut, while working at Foundation Imaging. How many 64 [New York World's Fair] buildings can you spot?" —
Doug Drexler).
And this is no matte concept. I asked TMP matte painter Rocco Gioffre about it and he said the painting was Matt Yuricich's work. This is reinforced by the matte line around the tram, which tells you it's an effects composite. It might have been an imperfect composite, possibly a work-in-prpgress, but there's no way of knowing what stage of the process this particular frame was from, as most matte shots were composited, reviewed, and reprinted with adjustments to exposure, etc.
OH! And the hillside isn't a painting. It's the cliff to the west side of Kirby Cove. I've photographed it. See?

(The image of the painting is a tad scrunched, and crops off the lower part of the cliff and the rocks in the water, which are a perfect match. Sorry about the backlight, the time of day was very different than when the matte plate was shot.)
The brief shot of the seal was simply to tell you where you were without the damned chyron they added to the DE to tell you the same thing. I'd have to look for the exact quote, but I'm pretty sure it's in
Return To Tomorrow that there's mention that they shortened the San Francisco intro to pick up the pace. The book is pretty straightforward about other things they changed for budget and time reasons, so I'm inclined to believe it over after-the-fact accounts.
https://en.wikipedia.org/wiki/Paolo_Soleri