The mobile launcher being moved to 39B this week has left me wondering about the BFR and integration. Payload integration has traditionally been done vertically, I think, and that's led to some issues with certain F9 payloads. I seem to recall early ITS renders had the ship being loaded vertically. I have to wonder, though, and I doubt there are answers at this stage, but how will the BFR be moved to the launch pad? How and when will the BFS be mounted? How will payloads be integrated into the BFS? Definitely not expecting answers to these questions, just things to think about until spacex reveals their designs.
Tl;dr pure speculation: jumbo transporter, horizontal initial integration, rotating satellite mount if needed.
Long version:
From the renderings, the BFR (first stage) lands back on it's launch mounts after each launch so it remains vertical (until serviced). Initial transport would be horizontal via barge from Port of LA. Need a bigger transporter (and boat).
BFS gets craned onto BFR for refuel missions. For the satellite version, payload mounting could be vertical (given enough room). However, BFS will have suffucient structure to handle being horizontal, especially given the aero braking delta wing design.
In the case of horizontal mating, they could put in a rotating satellite mount system so that the satellite is always vertical as the BFS rotates from horizontal to vertical.
Which also means they could make the grand daddy of horizontal transporters for the combined system. Comes in handy for system bring up and such, then no need for a VAB sized structure (at least vertically). In that senario, the launch mounts may detach from the transporter and fasten to the pad followed by removal of the strong back portion, or the transporter and lauch mounts attachment points are non interfering.