Well, of course. MUI has never been part of AmigaOS. AmigaOS already has a GUI system and it isn't MUI. So I'm not sure why you would put MUI into AROS instead of the official GUI system.
Well maybe you should take a step back to see what really has happened:
Hack&Patch were doing 3.5/9 on the cheap, scamming contributors left and right.
Doing those few actually new tools in 3.5/9 based on just plain GadTools+BOOPSI was no option.
Stuntz was to smart to give MUI away for free.
So they had to find a 2nd class GUI system that could be aquirred at next to 0 cost, and hell did ClassAct fill that bill.
The reality even today is that it is 100% possible (and not even hard) to setup a useable Amiga without ever touching ClassAct/ReAction. Try the same without useing MUI (yes even on OS4)...