I have tried TreasureTable changes myself, and as far as I can tell any changes a Mod makes to the contents of the TreasureTables are ignored. Custom additions do not apply either.
It is possible to change the contents of a container via the RootTemplate, but they can only point to pre-existing TreasureTables. It's also possible for custom items to use pre-existing Object Categories (ie SkillbookAir or Gold or whatnot) to show up in places where objects of those category appear.