The problem is I don't think the original f/x sequences exist anywhere in pristine condition.
The problem isn't the sequences, but the elements that make them up. The compositing techniques used at the time to combine the different parts of the FX images lowered their resolution, created visible matte lines and flaws, etc., and so they don't look very good in high definition. The problem was worse for TNG because the compositing was done on video, with even lower resolution. But in the case of TNG, all the individual film elements that were combined to make the shots still survived, so they were able to re-composite those elements in HD, essentially recreating the same shots without any loss of resolution from the original film elements (although they replaced elements existing only in video form, like many of the planets, animation, early CGI like the Crystalline Entity, etc. with new CGI). With TOS, however, the original film elements that were used to create the shots (e.g. raw footage of the ship, planets, starscapes, animated beams and energy fields and such) no longer survive, so there's no way to recomposite the original footage. Recreating the shots in CG was the only way they could do it in HD.