I guess, the problem is two-fold. First, most music theory used in education comprises only those national cultures that had been embraced by the Western classic academic music, that is, the Western church tradition and folk traditions of mostly Western-European and Central-and-Easter-European origin.
Second, while it is not the case that both folk and classic (religious, court, whatever) traditions of non-European peoples are neglected in modern music theory, the available theoretical treatment of them is just not ready for using in general education. Go notate gamelan for primary school pupils! And even some of non-academic musics popular in West and worldwide elude analysis and explanation by “school” musicology: some very flamboyant and memorable pieces may just lack elaborated harmony or non-trivial melodic line, their originality having rested mostly in e. g. the timbral roulades or micro-tonal or micro-rhythmic shifts or who knows what else.
At the same time, there are many reasons behind including native and grassroot musical material to students, first of all, not to turn music education into a tool of further levelling the diversity of global cultural landscape.
I do not think there is a simple answer to this challenge. Mechanistically adding “rebellious” material to the one traditionally used in the classes is not an option, for this would create an artificial hierarchy of literate and illiterate musics. Putting most or all the weight on oral modes of education, as Prof. Lucy Green proposes would deprive students of theoretical experience (and the joy of fusion of ear, throat, eyes and mind actions).
Perhaps this is a task for theorists to create frameworks of concepts and languages to deal with the actual diversity of global musical experience—those available to children/teenagers of school and college ages.