Also, remember, similar appearances do not necessarily imply that something is based on the same design. To (approximately) quote C.S. Lewis from Out of the Silent Planet:
He was reassured to see that the [alien] boat looked much like a terrestrial boat, but on further reflections wondered "What else could a boat be shaped like?"
The contemporary F-15, F-14, FA-18, Mig-29, etc. all have similar appearances--twin engines mounted below and beside the cockpit, more or less delta-shaped wings, conical nose with a bubble canopy, and a twin tail--and yet these are completely different designs by different nations. None was merely an "overhaul" of another. They have that shape because it is the best shape for a fighter jet that our current technology is able to identify and build.
And to cite a counter-example from Wing Commander--look at the WC1 and WC2 variants of the Rapier II. These craft, while based on the same frame, have some striking differences in appearance--yet this is a case of one fighter just being an overhaul of another.
That said, certain technologies do require certain shapes of components. See the above example of contemporary jet fighters. For another example, all WWII era radial engine fighters had a certain shape of nose (P-47, FW-190), while V- and inline engine fighters (P-40, P-51, Me-109) had a different shaped nose. So maybe the similarities you've pointed out between the Banshee and the old Rapier, especially around the engine region, imply that they may have used similar sorts of technology for their power plant, that was different from technology used for many other fighters. Certainly if that technology was very reliable, I could see the BW being interested. Of course, this is mere speculation.
We know nothing about their history and the only thing that ever suggests their use by the Confederation military is their appearance as trainers in the 'good' ending.
Is that even the Confed military that is using them as trainers? I didn't pay that much attention when I first played through the game (well, the second time I played through...the first time I got the bad ending...stupid Hawk), but I assumed that they were trainers for the Border Worlds military. I didn't figure that Blair, Panther, Maniac, et. al would just have been welcomed back into Confed after "betraying them" and especially shooting down Confed pilots, even after being vindicated at Tolwyn's trial. And after all they'd been through, I didn't figure Blair, Panther, etc. would really want to live out their restful retirements flying for Confed.
On the other hand, we know that Blair and Hawk do end up back with Confed (from Prophecy) eventually, so maybe I just wasn't thinking clearly.
Does the UBW get absorbed back into Confed after WC4, or do they retain their independence?