If there are real distinct semantics that were "abusively" unified by the canonicalization, the only safe way would be to create a second character that would have another combining class than the existing one, to be used when lexical distinction from the most common use is necessary.
So the added character for the modified vowel signs would have the same representative glyph, but would have the additional semantic "contraction" (clearly indicated in their name). This does not break the existing encoding of most texts, but allows a specific usage for contractions where the existing canonical equivalences would be inappropriate.
How do you envisage this getting into the data?
Often in Tibetan data capture, operators are keying in the appearance of a text and do not know what a stack represents.
So the data then requires expert review after input to verify and assign the semantic representation.
Peter

