The 10.9.2 rule is actually two-fold, that the longer word with “good” is either in the shortforms list or begins a word and is not followed by a vowel or y. ICEB decided that “goody” was a worthy addition to the list. The list takes precedence over the vowel rule. Therefore, it’s acceptable to use the shortform. There are other words that parallel this: goodie, goodun, goodyear, goodest.
According to the rules for list construction at the end of Appendix 1, words containing shortforms may be added to the list if the longer word retains an original meaning of the base shortform word. As for "must," it can refer to a musty state. "Musty", "mustier", and, believe it or not, "mustard", all have ties to this definition. (Mustard was originally made with must. Who knew?) "Mustang", "muster", and "mustache" have no connection to any definition of "must".
By the way, those rules for list construction are meant to be informative, not instructive. They are the rules that ICEB followed when constructing the list. They are not rules for transcribers to independently add words when they come across a word they think should be there.