Supersu works just fine on CM as long as built-in root is disabled. There's no issues whatsoever. And your Xposed point only applies to some modules that affect system apps or system frameworks such as GravityBox. Actually, many universal Xposed mods work better on CM than heavily modified manufacturer UI's such as TouchWiz. Also, you can do a lot more with xposed than to modify system apps or framework. You can hook into downloaded apps and do wonders. That doesn't affect the system in any way, nor will it have any conflicts with system behavior, was it CM or TouchWiz or Nexus or whatever.
Ofc it's highly dependent on which rom one is using. There's official CM and then there's many roms built on top of it. Everything has always been smooth with Xposed on all CM roms I've ever tried. Only issues I've ever had with Xposed was with AOSP based rom.
Ps. You want to know why Xposed is not supported by many rom devs? - because most of the times the errors users get with Xposed are not related to Xposed framework nor the compatibility with the rom, but to the modules the users have installed. It's not the rom dev's issue if module A breaks something in the rom itself, it's out of their control.
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