Unless your alteration is a legit parody, you are diminishing the original by subjecting it to change that was not intended by the makers.
Say for argument's sake somebody decides Spock shouldn't die at the end of TWOK. Well, you could run the shot of him going through the revolving door in reverse to show him exiting successfully after mixing all the crap, then dub over McCoy saying "it's that green blood of his" from OBSESSION and voila, different movie. You go to Kirk & his kid in his quarters after showing the burial ceremony (a voiceover indicating it is for Peter Preston) and you're done. You've destroyed and distorted all the resonances and what made it work in the first place, and so even if you say the original is still there, you have diminished it.
So when Lucas decided to re-do some the effects for the original SW trilogy, thats ok? (Note: I have no issue with the changes)
FX is a balancing act between what you want and what you can afford. So perhaps for some of TOS-R we got the FX they wanted had they the time & money to do.
If you consider the spec eds of SW to be parody, then I guess it is okay. I think the changes are bad, but I don't care enough about STAR WARS to raise more than the occasional stink about it, though it troubles me that STAR WARS was a film selected for 'preservation' -- and yet the originals (or something fairly close to them) that are available for viewing now are limited to DVDs that are just copies of THX laserdiscs.
(if I'm wrong about that, if they've issued a new set of 'original' versions for BR, please correct me.)
The retcon thinking associated with, 'this is what they would have done if they had more money or more time' is as much a matter of revisionism as truth, probably moreso. The changes Wise indicated he wanted to make in TMP in the year or two after it released don't correspond with the changes that turn up in the alleged director's edtiion, even though that was promoted (and largely accepted) as 'this is what he would have done if he had the time.' It is much more likely this is SharpLineArts' vision of what TMP was supposed to be, though it incorporated some more mundane continuity bits that Wise DID ask for.
Wise DID have the time on the original TMP to keep Matt Yuricich's original Vulcan matte painting, which was tons better than what went into the theatrical version OR the cutgame looking thing cobbled together for the DVD DE ... but he apparently chose not to include it, god knows why.
Except for the occasional total misfire FX-wise on TOS (TOMORROW IS YESTERDAY is I guess the prime example), I don't think there's a lot of ship VFX that really would have benefitted from tons more money being thrown at them. Maybe reshooting some ship passes so there wasn't the really bad bleedthrough or chattering on the mattes, but shoot, if those were really bothersome they could have used other shots (like those near-perfect close shots of the ship pivoting that really show the nacelle caps to glowing effect.)