Flaps don't matter in CFS2 when it comes to take off. All stock aircraft but the P-38F don't have any more lift with flaps out. All the flaps do is slow you down with the drag they make.
Au contraire, mon ami. Actually they do matter, but the original defo air files of the stockers were "robbed" of
realistic lift and pitch in order to make the stockers more AI friendly in landings. For those unfamiliar with the topic, there are three factors in the air file assigned to CFS2 flap dynamics: drag, lift and pitch. Pitch and lift play a large part in controlling a model's angle of attack (AOA) on flap deployment. This is probably most noticeable in all 1% fighter birds, which were flight-designed outside of the standards of CFS2 stockers and tend to have an extra helping of effectiveness in all three factors. Check out record 1101 in the air file for more details.
I've had a lot of experience with making addon aircraft designed primarily for player usage (with realistic flap dynamics) behave better in AI landings. What i've found is that the more realistic the flap lift and pitch, the more difficulty the AI have in their angle of attack in landings. If the pitch is set too high, the AI will go into a severe nose down position as they roll down the runway after touching down as an overcompensating measure. If the lift is too high they tend to flare longer over the runway before touching down, which causes them to touch down and roll much further down the runway and sometimes well beyond it before coming to a full stop. I've done a lot of testing to confirm these findings. Take your most "realistic" flight models out on a "land at base" mission, land your plane first, brake hard and park as close to the runway's midpoint as possible before the first wingies touch down and watch them perform their landings to full stop...things can get a little weird. In some instances i've even found that the designer had inadvertently set the flaps with negative pitch, which exacerbated the AI "pitch down" even worse on landings.
And i might add that these things occur even in models that clearly show no visible flap animation in the AI when landing. Even without the animation, the sim engine still uses the flap settings in the flight dynamics of the airfile to set the degree of angle of attack and drag applied during landings. Its one of the reasons why i don't rely solely on Airwrench's final output when doing air files. I go in and hand edit the flaps to keep things moderated for the AI landings.