That is truly a great idea! With that, we can even have both historical and alternative historical "what if" with the secret project aircraft from Germany, USA, UK, Soviet, Japan, and other countries flying as realistic as possible.
As long as you have Reynolds Numbers or equivalent for wing airfoils. Some of the necessary data isn't available for poorly documented or "paper" aircraft.
More practically, if the game engine allows you to modify flight model info on the fly, is the potential to add and subtract equipment, alter mass or CoG based on damage or consumption of stores (or even movement of passengers), and to change flight performance based on damage.
For example, let's say you're flying a B-17 and the nose compartment gets a big nasty flak hit. The blast kills the navigator and bombardier, blowing their bodies out of the plane, and also blows away much of the nose ahead of the cockpit. This creates massive amounts of drag and changes the plane's CoG to make it tail heavy, but also reduces the plane's total mass by a good bit. Let's also say that the blast forces part of remaining nose bits downward, creating a sort of an airfoil which makes the plane want to fly upwards in addition to its other problems.
If the FM allowed for dynamic changes to mass, drag, lift, etc. then you could realistically handle the crisis by ordering equipment to be jettisoned and crew to be repositioned to fix CoG problems, dropping bombs to reduce overall mass, setting trim tabs and applying constant pressure on the stabilizers to keep the plane from climbing, etc.
On a more benign level, you could easily add gun pods, equipment, etc. by modeling them as different bits of the aircraft with their own FM & DM. For example, you could add or remove RDF loops, radios, radar equipment, etc. or modify baseline aircraft with chemical or water tanks, MADD "stingers" or AWACS saucers.
It could also allow better modeling of composite aircraft.