CyanogenMod Phones

[Salem Kakish]

I just rooted my GS4 and flashed CyanogenMod on it using the CyanogenMod Installer. Don't worry, nothing bad happened to my phone but I do have a question about the apps. I've heard about the Oppo N1 CyanogenMod Edition and that it is the first google certified CyanogenMod phone. That means that it's Play Store is the same as any on any un rooted phone. My question is: since I have a phone that has CyanegonMod on it, what is the difference between the apps that I download through the 'CyanogenMod rooted Play Store' and of the normal 'un rooted store'? Do they receive updates at the same time? Are the apps the same? Cause I've noticed that all the apps that I've downloaded through my gs4 that has CyanogenMod installed on are .apk files.

I would really appreciate if you guys would respond to my question.
Sincerely,
Salem