My best guess for why HTC decided to call it a Spitfire Mk XVI rather than a Spitfire LF.Mk IXe is because while most WWII aviation enthusiasts are used to subvariants of Bf109s, particularly Bf109Gs, being massively different, most people think of a given mark of British aircraft as being all the same and HTC likely wanted to avoid confusing less informed players by having a Spitfire F.Mk IX and a Spitfire LF.Mk IXe.
I even see authors mistaking the clipped wings as being relevant to the LF designation. It really isn't all that complex, not nearly as varied as Bf109Gs, but for whatever reason the Spitfire Mk IX family throws people off.
Spitfire Mk IX family:
Spitfire F.Mk IX = Merlin 61 or Merlin 63, universal wing
Spitfire LF.Mk IX = Merlin 66, universal wing
Spitfire HF.Mk IX = Merlin 70, universal wing
Spitfire LF.Mk IXe = Merlin 66, e wing
Spitfire HF.Mk IXe = Merlin 70, e wing
Spitfire Mk XVI = Merlin 266, e wing
EDIT:
Bubble canopy Mk IXs, Mk XIVs and Mk XVIs missed the war for all practical purposes. It would be kind of like adding the Me163 or Ta152. Well, not quite as bad as the Ta152.