There are plenty of rogue traders in the 40k novels with only one ship. Included would be Orrelius from the Ciaphas Cain novels, who only has one ship, and Tobias Maxilla, who also just has the one ship. Both have them have been rogue trader for ages, and yet only have one ship, and it's unsure what size vessel that is. So it's entirely reasonable for a RT to only have a single ship.
Plus, I wouldn't look into Battlefleet Gothic too much, that's the same game that says cruisers are eight times as tough as escorts, and escorts don't have criticals, they just die, which is totally unlike the ships in Rogue Trader. Best not to use miniatures games rules as a basis for an RPG, because miniatures games are simplified to an amazing degree compared to RPGs (as demonstrated by the power, range, etc of some weapons in Dark Heresy/Rogue Trader).