Except the change in the Klingons' appearance is not diegetic except in "Trials and Tribble-ations" and "Affliction"/"Divergence." Every other time it's happened, it hasn't been mentioned or had any effect on the story. When Kor, Kang, and Koloth showed up in "Blood Oath" with ridged foreheads, nobody in the story remarked on it; it was treated as the way they'd always looked. That's a textbook example of a change that isn't part of the narrative
I always liked that they did that for the Klingons though. I mean, they did kind of back themselves into it with "Trials and Tribble-ations". I have to admit it was kind of comical when they were speculating why they looked different (and of course the line "THOSE are Klingons???"), I think partly because some fans have been speculating on that for years. And that was the one design that has been speculated on for years, including a number of novels. You're right that other aliens have changed...some relatively minor like forehead ridges on Romulans, some a bit more significant like Tellarites...but it seemed most fans, including myself frankly, were willing to just go with it either because the change was pretty minor and the overall product was similar enough to the original, or the aliens depicted weren't a significant part of the Star Trek universe, usually because they weren't seen that much.
But Klingons were probably the most significant change to a popular alien in Star Trek. In that case I thought it wasn't a bad idea to offer an in-universe explanation for the change in appearance. They were one of the few aliens where fans and novel writers had speculated on the change in appearance in Klingons for years, why not add something in story. "Trials...." gave them an opening in a sense, since they acknowledged the difference, and while it took a few years, they finally followed through.
Retroactively, when it comes to Kor, Kang and Koloth, I generally assumed they finally found a cure to the Augment virus and the Klingon dominant features manifested themselves again, perhaps decades earlier (hence the lack of any reaction to their 'new' appearance). If I recall correctly I believe the Excelsior novel "Forged in Fire" said as much.
It's one reason the Giger-Klingons in Discovery bug me. They went to all the trouble to tell the story of how the Klingon appearance changed and that seems to have been blown up again.
