[@Eisenhorn]In terms of an armament, something that the aircraft would have during those times. Take your note of the Supermarine Spitfire, it would more likely just be the regular quad-built in .303 (7.7mm) Browning Machine gun configuration, but very few had been fitted to use missiles. Ammunition storage may be raised, to drift away from total realism.

As for performance, I'd say almost no change to the airframe, shape or mechanisms, though I'd say the same for engine components and such. Colour can also be changed, based upon where the aircraft was sent from before the Fall of Europe (I.e. Africa, Europe, Asia etc). The standard customised insignias are also up for the taking. 

For bombers, all of the above are the same, except with the difference of defence turrets. Within reason, the bubble, rear, front (etc) gunners can have a different configuration to what they might have usually been fitted with, based upon what you think is more useful to it.

Close Air Support/Fighter combinations, such as the Hawker Hurricane variants, can be fitted with rockets. Interestingly enough, there was a variant of the Hurricane that was also fitted with large Anti-Armour cannons as well as the Machine guns, which did jolt the craft around a bit.

If the new variation of aircraft, basically their own creation, then the same goes for all of the above. As long as it is usable, reasonable and reliable, them there shouldn't be any issues. Hope that helped!