I can see this being the case to an extent. Since the technology will be integrated (aka attached) to each seat they will likely need to take a train off and switch out as they sort out issues with VR, This would be better than shutting the whole ride down, but would still affect capacity...likely still better than VR working...lol All joking aside I hope they can get this done right as I've heard nightmares about every where else who is/has tried.
What they are re-working is the width of the station to allow additional ride attendants/Ambassadors on the platform to help with loading/unloading & cleaning the headsets each cycle. They will likely widen the platform on the station entrance side by moving the air gates/rows back to allow less passengers in the station with a grouper assigning rows. Each seat on each train will have the VR headsets attached to them so there wouldn't be a need for a separate line. You either use it or not when you get in your seat.
Also From Screamscape:
SeaWorld Florida