ORIGINAL: el cid again
This is a difficult matter in several respects - as various valid principles conflict.
In general, I think an aircraft should be represented by its most common production model - which is approximately what you are advocating. But I don't like an aircraft model to have anything whatever it didn't have the first day it was operational - since it is available to players in that form and they will shamelessly upgrade to that standard. If there is sifficient difference - it warrants a new type.
For aircraft such as the B-25C/D and A-20, isn't wasn't long before every single aircraft arriving in Australia was heavily modified. By late 1942, all 5th AF A-20s and B-25s had Pappy Gunn's modifications. Repair depots in other areas of the Pacific followed suit soon after. Even though they were not produced with the package guns and nose guns, they all had them by the time they reached combat.
The US had many modification depots to alter aircraft after production. In some cases these depots were in the US, in others, they were near the combat zone. In Anchorage, the USAAF had a facility that modified every aircraft arriving for Arctic conditions. In the case of those modifications, there were no changes that would be reflected in the game except possibly some performance decrease. All Alaska based aircraft were a lot heavier because they carried extra electronics for blind landing in the Aleutians.
In Australia, bombers were modified for low level strafing and attack roles. Similar changes were done in India for fighting in Burma.
When the B-29 campaign switched to low altitude attacks, all B-29s arriving on Saipan had their turrets removed.
In the US, the USAAF set up a modification center in Cheyenne, WY to modify all B-17s coming off the production line. This depot added some equipment and changed out the tail gun position for what became known as the Cheyenne Turret. All late model B-17Gs arriving in Europe and the Med had this turret installed before leaving the states, but after production.
I think it is best to provide the most common version to see combat. Yes, players will end up with a bit more capable aircraft for a few months when first introduced, but overall, I think this is best. If players are only given the production varient, without common field modifications later in production, then over the long haul, they are getting short changed. In the first few months after introduction, the aircraft will not be used much because there won't be that many of them available, except for a few types with huge production quantities.
Bill