You may backup user apps + system data but when restoring I'd do it differently.
I think it's better to restore through TB only user apps first, reboot, and then restore only some system data you may find important (Wi-Fi passwords, sms, call log, etc), not all system data as TB can mess with your restore and put you on bootloop (i already made that mistake a few times)...
And yeah, a clean install is always better. I normally take less than 30 min to clean install and restore everything...
Lately i've seen a bunch of people sayin that o xda, ex here.
I assume the one how wrote that made enough research to reach that conclusion. For many years i read people arguing and i think it's almost 50/50.
(Hope he didn't write that just to call for attention...)
As for the CPU that's weird bcuz i was using stock rom and after each reboot it kept the governor and scheduler, not the default values.