AFAIK you can remote control via VR and with that I don't mean jumped-in.
In AR remote-control means your comlink and its Command program projects "control instruments" in front of you and you use your AR glove to manipulate them and your cybereyes or AR goggles to see them.
In VR your comlink and its Command program create a whole "control environment" with the instruments around you and you use them and get the +2 for using VR.
With this interpretation I would say Remote Operation specialization would be used in everything you roll with remote control (so Command + Pilot).
It's unfortunate that they didn't use the words Remote Control for the specialization.
I would think that jumped-in (being the vehicle) and remote control (manipulating an AR or VR steering wheel etc.) are very different and that you could add a jumped-in specialization if you as the GM would want to. But I don't think you can use both with the same specialization.