To me it makes more sense that you write the story first if you're going to be requesting a ship that is purchased from a Guard system belonging to a faction. For example, if you wanted a Liberty Rogue Gunboat and you entered Cassini without first getting permission from the LR-, we'd blast you to pieces on sight. We'd also assume the ship was stolen if it was not being flown by someone with an LR ID/IFF or Molly ID/IFF, since the ship is only sold in the LR and Molly guard systems respectively.
I believe most Gunboats are now sold inside Guard systems.