Intended. They're not "real" Commanders.
Maybe I should rename them or something...
I suggest Muton Elite, that worked for EU2012 and it'll work here too. Or Elite Praetorian, it'll fit in with the leader class being called Praetorians.
For the black spheres, I could imagine them acting as a key of some kind leading to the stronghold of the Cult's demonic masters or perhaps the secret to how the cult can open hell portals, with the general gist from there being that cutting off the Cult's ability to call up the legions of hell will leave them as nothing more than a pack of disorganized thugs.
Also after the final Cult of Apocalypse mission I suggest adding commentary from staff of choice along the lines of "maybe now those monsters will stick to torturing bad dead people instead of good living ones".
P.S. Have you considered adding something we could spend lots of money on in the late game to endgame? I'm sitting on what was a 9-figure balance last time I checked and there's nothing useful I could spend it on- as much as I like the buffer for when most of my funders get infiltrated and I use up my last decrypted key, it's a little embarrassing to have so much money.
ADDENDUM:
From the changes you made to the Assault Plasma Grenade, line 11842 of items_XCOMFILES.rul:
categories: [STR_SHOTGUNS, STR_HUMAN_TECH, STR_SONIC, STR_CLIPS, STR_UNDERWATER, STR_SPACE, STR_LAND]
I don't know about you, but the Assault Plasma's Elerium Grenade still should not be classified as a shotgun, a sonic weapon, or usable underwater. You might want to go and fix it again. At that matter, the regular Assault Plasma clip has STR_LAND listed twice on it. I've whipped up a PR on GitHub that should fix both of those problems, so merging it will squash the bug there for good.