That doesn't hold the weight you're expecting it to. The lack of the "director edition" of the first Star Trek movie wasn't about creative choice or going back and righting a wrong (the director edition actually tried--and did well--to complete effects and make the movie more coherent, all of which was caused by studio meddling at the film's original release. There weren't many complaints about that being the only version available on DVD) (Wrath of Khan is the only other one you could be referring to as having a director's cut on DVD, but it also had a theatrical DVD). The only reason they were released on Blu-ray as they were was for technical and financial reasons. The director edition of The Motion Picture was done entirely to SD elements and would have to be redone from scratch for an HD master (much like the 2004 and 2011 Star Wars SE's changes would have to be redone if a 4K transfer of the 97SE conformed o-neg exists), so as to pop the movies out quickly and cheaply to Blu-ray, they just scanned existing elements (didn't even clean up dirt and scratches much). Don't be surprised if they put out new editions sometime down the road.

@darklordoftech I'm not trying to argue that you didn't answer the question, I'm just sarcastically pointing out that what you say are reasons to keep SE changes don't necessarily hold as much weight to others. I particularly don't see any need to keep any SE changes, and if something in the PT clashes with OOT, then the PT should be changed, and then maybe it would be less shitty in the process.