I think the point is, that opening "muimaster.library" will point to MUI on a MorphOS machine and Zune will be unnecessary. You'd have to rename the library so it would be incompatible with MUI apps everywhere expecting to open "muimaster.library". In short, the best solutuion would be to make Zune compatible with MUI for all AROS flavors and OS 3 since there's no point in registerring Zune, and OS 4 could use a future Zune that is compatible with MorphOS' MUI versions.
BTW, I'd appreciate some help with MUI Builder some time. I have little experience coding GUIs and would like to add support for the NList family of MUI Custom Classes.