So do the original and Okrandized spellings of "Klingonaase."
Yes, which is the point. In neither case is it "purely" a matter of orthography, because in both cases the change in spelling would change the pronunciation as well.
Also, Okrand's explicit intent was that "Klingon" was an in-universe anglicized approximation of
tlhIngan. T'Kuht/T'Khut is different, since it's probably just a case of Duane misremembering the previous spelling, or deciding her version looked better. She wasn't suggesting it was an alternate spelling; it was
the spelling in her version of the universe, as distinct from Jean Lorrah's version.
(Then you have A. C. Crispin in
Sarek calling it T'Rukh but mentioning that it had several different names, which I take as an oblique reference to the other names it's been given in various works.)
And to a hypothetical native Vulcan speaker, "T'Kuht" and "T'Khut" would either be equally correct (possibly owing to a regional difference in accents) or equally wrong (the native pronunciation being impossible to accurately Romanize).
Not necessarily; it could be that one is simply a typo, like the tendency of Americans to misspell "Gandhi" as "Ghandi," because they're unaware that the H isn't silent.
(I was just thinking earlier about how Japanese speakers must wince when they hear English speakers pronounce Tokyo as "To-ki-o" when it's actually To-o-kyo. I realized that was probably what the Sentai series
Carranger was parodying when it had all aliens mispronounce "Chikyuu" (Earth) as "Chiikyu," doubling the length of the wrong vowel.)
(clue: "Neanderthal" has the same problem for native English speakers who haven't taken German).
I've sometimes seen it spelled "Neandertal" to clarify the pronunciation.