Another issue with third party ROMs is that some software builders actively block or sabotage them. For example, the AT&T's Uverse streaming service will detect whether you have a rooted or third party ROM and stops working. The Netflix goes only up to 480p resolution on a non-stock ROM. "Fixing" this probably involves editing build.prop and hiding your root, but I haven't tried it recently.
Android Pay also has issues with rooted phones (and, by extension, custom ROMs), but I have it working on an Asus Zenfone 2 running CyanogenMod 13. A combination of Magisk and phh's Superuser successfully fools Android Pay into full functionality. You might want to give them a try with other root-averse apps.