If weird annotations can work for slightly different phonemes in Orthographia Bohemica and for Zamenhof, I'm sure you would be able to use them for tones as well.
You can, it's how it's done, but it means someone who knows any other language using the Latin script still can't read it.
A speaker of French, Polish, German, Hungarian or Turkish can muddle through trying to pronounce another European language using the Latin script and get 95% of it but will have no idea of how to read Vietnamese.
