Arabs with Israeli passports are routinely searched and investigated by intelligence agencies, and in the occupied areas Arabs WITH Israeli passports are not allowed to visit certain areas (multiple sources online, including the recent Louis Theroux documentary). This is the very definition of an apartheid state.
No one with an Israeli passport is allowed to visit Area A of the West Bank, regardless of their ethnicity.
One case is an assertion of sovereignty (whether we agree or not), the other case is apartheid.
Areas outside of Israeli control where Israelis are not allowed to go is irrelevant when discussing about whether Israel is an apartheid state or not.
Actually you said
> in the occupied areas Arabs WITH Israeli passports are not allowed to visit certain areas
But in any case, since you also said "multiple sources online" perhaps you can link one so we're talking about something concrete and not just vague insinuations.
It is trivial to find more sources than the one I already mentioned, there is a very very long wikipedia article as a starting point. I'm afraid you do not care about seeing what is going on, you care about dismissing opposing opinions.
https://old.reddit.com/r/IsraelPalestine/comments/v8s88z/ara...
https://www.quora.com/Why-can-t-Israeli-Arabs-live-in-Israel...
Sounds like you have more than enough to get started.
Or maybe stay with reddit and quora. Up to you.