Why is there such a performance difference (aside from roll) between the two in game?
The Spitfire Mk IX in AH is the much earlier Spitfire F.Mk IX with a Merlin 61 engine. That engine is less powerful, and supercharged for best altitude at about 25,000ft.
Basically:
Spitfire F.Mk IX, Merlin 61 - mid 1942
Spitfire F.Mk IX, Merlin 63 - early 1943
Spitfire LF.Mk IX, Merlin 66 - mid 1943
Spitfire HF.Mk IX, Merlin 70 - mid 1943
Spitfire Mk XVI, Merlin 266 - mid 1944 (Spitfire LF.Mk IX in all but name)