First of all, I don't think that having a single launch bay has anything to do with having a fly-through deck or not. The old discussion about the WC4 Lexington having two launch bays but only one fly-through hangar comes to mind (I don't remember seeing the Lexington launch ships from the rear end of the hangar). At least when I started modelling the Firekka, the general consensus was that a launch bay is where you ready a ship for launching, and that as such this was independent from the size of the flight deck or how many openings it has.
Second of all, I modelled the ship according to the cover art and to what I could gather from descriptions in the novel, but also (as with some other Standoff ships) to try to bring WC2 and WC3 designs closer. The fly-through deck is there because I couldn't find a reference that said it shouldn't be there (although it seems someone ended up finding such a citation in ER), and because it'd make WC2 and WC3 designs seem like they blend in better.
Finally, on a more practical note, the fly-through deck is what allowed us to use the automatized WCP landing routines (this is the only reason the Lionheart also has rear entrances to its hangar). We just tell the game's engine to have a certain ship land at a certain capship, and it does the whole process of switching cameras, etc automatically, like it did with the Midway and Cerberus.
We use an invisible box to tell the engine where the hangar is relative to the rest of the capship (ie: the Lionheart's hangar is off-center and lower than the rest of the ship, while the Firekka's is centered and only a bit lower than the rest of the ship), but I don't think we are able to change the actual approach angle (so the ships always start their approach angle a few meters straight behind the point where we told the game the hangar's entrance was).