The problem with 6 and 9 is that there are 2 very unrelated sounds for t and d in Arabic. Mixing them is a hallmark of non-native speakers tell signs and to an Arabic speaker’s ear sounds broken. It’s like when German speakers mix th and z sounds in English. It’s very jarring to the ear and requires you to parse the same word you’re reading twice in your mind to tell whether it was 6 or t (or 9 or d) especially that very similar words might exist like 6atreb and tarteb or trab and 6arb. I usually don’t use 6 and 9 either except when I want to emphasis the 6 or 9 sound in a word.
Kh and gh are problematic mainly because you’re relying on the special rule in Arabic that you can’t have 2 constants like k, g and h sounds after one another in a word. You’re relying on the wrongness of a kh or gh construct in Arabic to realize they must be standing for something else. I prefer them tbh, but I get the desire of some to have symbols for them.
غ Is sometimes 3’ but I have seen more gh than 3’ especially that 3’ mixes the academic romanization with the “Arabiz” romanization