He and his team made some very dramatic changes to other parts of the film, but they left that sequence alone. Why do you think that is? (I don't mean that rhetorically, I'm legitimately asking.)
Very dramatic changes? Let's keep things in perspective, or we'll run out of adjectives. An example of a very dramatic change would be what was done to Fatal Attraction after its test screenings, when the ending of the story was changed entirely. Nothing like this happened here.
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The TMP DE does not represent a realization the version that Wise wanted to make when the film was originally released. We know this by the remarks Wise made around that time. Casting the TMP DE as a realization of Wise's original vision would therefore be untrue.
I doubt very much that making the cloud 2AU in diameter instead of 82AU in diameter and inserting a TOS shuttlecraft were changes proposed by Wise. I'm open to correction, but I very much doubt it. Ergo, the TMP DE project was not just about Wise making the film he wanted to make, even if he had changed his mind in the intervening decades about the pacing of the drydock/starship reveal scene.
Third, there were no major changes to the structure of the film. There were scenes padded, trimmed, VFX replacements, new mattes, things hidden such as the universal translator text (

To really answer the question you ask, we would have to know the parameters laid out by the people footing the bill, and I don't know what the contracts say.
Absent that information, my take is that TPTB wanted a new version of the movie that would sell discs and wouldn't be too expensive to produce. Redoing a showpiece scene like the drydock scene strikes me as something that would have cost much more than what they were willing to pay.
Moreover, when you get right down to it, you could probably improve the film substantially by chopping out 20 minutes of it or more. And I would certainly have recommended dialog changes, too. But that would require a major reedit, maybe bringing surviving actors back into a sound studio.
In other words, really fixing the film, giving it the fixes it actually needed, was never on the table. The drydock scene, the cloud exploration scenes, they were liabilities going into the project, the sources of common complaints, but they were not actually the most acute problems.
The DE was, I think, about fixing the low hanging fruit that could be tweaked easily and relatively inexpensively. It wasn't really about giving the film a proper fix.
The great film it could have been is a version that will never exist, that sadly no one can ever see.
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