While recreating the mainhall, it was brought up that FS1's Galatea mainhall always featured the Herc, even when the Herc wasn't built yet. So I made an alternate (B) Galatea version that featured an Apollo for that chunk of the campaign. The same is true of Bastion. There is one little story arc where the player is on the Bastion before the Herc is built. That version of the Bastion contains Valks on the racks instead. So you have Galatea-A and Bastion-A which match the original retail ships and the Galatea-B and Bastion-B which feature alternate ships.
As for question 2.. you'll have to ask the FSPort team. I'm not longer a part of it and have no idea how they intend to implement different music (or mainhalls for that matter).