Isn't the real answer that it has nothing to do with the units under command, and is simply that RAF officer ranks follow RN ones (ignoring Plt Offr and FgO)
Flt Lt = Lt
Sqn Ldr = Lt Cdr (exception, but a Major in the cavalry is called a sqn ldr)
Wg Cdr = Cdr
Group Capt = Capt
Air Cdre = Cdre
The progression of Flt>Sqn>Wg>Gp doesn't follow (and really, hasn't ever followed) what they command in terms of units. How many RAF stations with a Gp Capt have had two multi-sqn flying wings under command?
Of course the above ignores silly titles like Admin Wg, Ops Wg etc on a station.