I think that, if anything, Transjordania will prove that ethnoreligious cooexistence based on mutual respect and autonomy is possible - and, if it succeeds militarily and economically like Israel/Jordan did OTL, that it's even more desirable than partition along ethnic lines. Pan-Arabists will strictly oppose this model, as it goes directly against the dream of a pan-Arab - and for Arabs - state from Morocco to Iraq, but it will be extremely attractive for ethnic minorities like Kurds, Copts, Assyrians and Berbers, and to a lesser degree to religious minorities like the Druze, and Lebanese Christians.
As for support from the Transjordania for these kinds of autonomist rebellions, I believe it is extremely likely, taking into account OTL Israel's covert support for those same groups (Iraqi Kurds, Lebanese Christians). If the conflict between Transjordania and the pan-Arab states continues (and there's no reason to think it wouldn't), I see Transjordania (with western backing, perhaps) supporting Autonomist revolts. TTL's middle east might be a three-way conflict between non-Islamic, non-Arab composite Nationalism championed by Transjordania, Arab Socialist Nationalism championed by Egypt, and Islamism Championed by Saudi Arabia.