The Just Android OS is usually the factory OS that you can ask for support from maker and your cellular carrier. The other is a rooted phone that maker and carrier have yet to embrace.
I have had no reason to root a phone yet because the phones I buy are unlocked.
Do you need support? would be the question you must answer.
Which one to prefer and Why?
Smartphone with "Cyanogenmod along with Android OS" or just "Android OS".