A Tibetan dictionary cannot be searched the way an English one can, because the first letter written is often not the letter the word is filed under.
Words are ordered by the root letter, the ming gzhi, which is the letter at the centre of the syllable stack. Prefixes are stepped over. Superscripts are stepped over. Only when the root letters agree do the other elements come into play, and then in a fixed order of their own: superscript, then subscript, then vowel, then suffix. A syllable written with five letters may therefore sit in the section of the second letter written, or the third.
The practical consequence is that a reader has to be able to parse a stack before it can be looked up, and parsing a stack means knowing which letters may occupy which slots. That is why the five prefixes, the ten suffixes, the three superscripts and the four subscripts are drilled early: they are not trivia about the alphabet, they are the index.
Modern dictionaries and search interfaces vary in how much of this they hide. Some accept a Wylie string and sort it for the user, some expect the root letter, and some offer both. But the underlying order is the traditional one, and any Tibetan reference work, from a canonical catalogue to a word list at the back of a grammar, assumes it.