The "it's not gone" argument ignores the core of all this -- the issue of tampering. Except for kids' books, the whole interactive choose your own ending of storytelling has largely flopped (and it is a good thing, because who wants a MOBY DICK where Ahab gets a bionic leg and then stuff his old peg down the whale's blowhole?)
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.
But none of the changes made in TOS-R go beyond the cosmetic, so it's an unfair comparison.