If you send me an email, I’d be happy to share some papers that might be useful for the modeling.

Correct, but almost no aircraft has a full span flap – the flaps are towards the root, so they do change the lift distribution away from the tip and towards the root.
Anyway, the AoA is simply a stand-in that is not used for the wake generated by the flightmodel aircraft – here we know the actual lift distribution! We know exactly how much the flaps contribute. But we don’t for an ADS-B target or a network aircraft. There we need to make a few educated guesses as to whether they are flying with flaps or not, and for network aircraft we can at least estimate the AoA because we know the body angle for the 3D model and can derive the vertical path from the 3D position over time.
Honestly, I think the effect is probably moot anyway given the low resolution of data we are likely to get for non-flightmodel aircraft. Live Traffic for example only supplies four different types of aircraft at all, one for each ICAO wake category, so every aircraft in the same category will leave exactly the same strength of wake. Which is probably fine for educational purposes – i.e. don’t fly a 172 through a wake left by a “heavy”. You are going to end up upside down, whether the wake was weakened a bit by the flaps or not.

I checked the new wake turbulence datarefs, but I think AoA should not influence wake strength per se.

If lift, air density, TAS and wingspan are known, then you can derive an approximate wake strength (in the simplified hypothesis of elliptical lift distribution).

So, for example, full span flaps should not influence wake strength, even if they change wing AoA.

In real life, flaps do influence wake strength mostly because they’re usually not full span, so they shed additional vortices mid-span and divide the strength among more vortices.

I’m not sure what the decay is (that’s Austin territory) but I can tell you for sure that an extended Fowler flap does not leave its own sub-wakes at each end of the flap element. With flaps extension, the lift is generated by a bigger surface at a lower AoA, which lowers the overall wake intensity as you extend the flaps, but it does not create additional smaller wakes for the flap element in X-Plane. The condensation you see trailing the flaps is a particle effect, purely visual.

I did a bunch of undergraduate and Master’s research on this topic, which is why I am particularly interested.

(If you know the Kutta-Joukowski theorem) you forgot to say. 😉

lift / (air density * TAS * wingspan);

(The formula above can be easily derived).

Formation flying works the same as in real life, too: Try not to hit the other guys wake. We tested this with aerial refueling, which is definitely a form of formation flying. As long as you stay where the real plane stays when being refueled, you are clear of the wake of the tanker.