Brightline as a whole can have express trains and "local" trains.NYC has been able to survive with express trains that skip stops and local ones that don't. So does Amtrak with both Acelas and Regionals. Not every stop needs to have every train.
The ROW can accommodate another service, ie: Sunrail and Tri-Rail with their own stops that Brightline has nothing to do with.
In the first scenario, this will only be useful if there are bypass stations. IE: Want an express from MIA to MCO with a stop in FLL? That's fine, but if you don't pass any other trains along the route, you'll still get to Orlando after the previous train no matter how long the ride takes.
In the second scenario, you will have completely incompatible platforms, if I understand correctly. You don't want a closed-gated train using the same platforms as an open-gated train. That, and commuters use low platforms and Brightline uses high platforms.
I guess, because by definition, shared commuter/Brightline stations will have different platforms, these will be passing stations so Brightline can hop scotch over Tri-Rail. If Tri-Rail thinks they are going to get 18 stations within Brightline's 3/4 between MIA and FLL, then just about every exclusive Tri Rail station may need a bypass track for Brightline. Maybe not all; depends on the scheduling and frequency of each.
Back to the first scenario - moot point until they decide on the new stations, but Boca and Aventura should be places where the "express" could overtake the "local" along with perhaps Jupiter and Cocoa.