Mechanically there is no difference between remote control via VR and jumping in (except the control order, dice pool modifiers for hot-sim as well as some vehicle related thresholds and limits).
However, it appear as if the book does make a difference between Vehicles and Drones. This is even more apparent if you look in Rigger 5.0 where for example upgrading Drones is a completely different process than upgrading vehicles.
SR5 p. 183 Gunnery
Vehicle-mounted weapons are fired using ... Gunnery + Logic [Accuracy] for remote operated systems.
SR5 p. 238 Control Device
firing a drone-mounted weapon at a target requires a Gunnery + Agility test
This reading is also supported by all existing examples I could find. Since there have been no errata on the subject (at least that I am aware of) the above should probably be considered rules as written.
I can't say if Missions specifically use other rules or not, but if Missions is pointing at core then the above is what they are pointing at.
