It's an interesting idea. I would be concerned that balancing the to-hit modifier against mitigators might be difficult - it'd be easy to make them either too useful or too situational.
I think it would make the most sense to have an HP reduction instead of armor reduction, due to the vulnerability of the flight-granting elements (wings, engines, H2 cells. . . ), and heavily-armored flying units are a common SF trope. Spitbaling a 75% modifier for HP. Size-equivalent AV vs vehicle armor/HP auto-kill on hit already, so, there's no real change in vulnerability to same-size weapons. However, this makes a given weapon system a threat to the next higher vehicle size - e. g. it almost doubles the effectiveness of medium AV vs 75% Heavy HP. It also improves the utility of autocannons a bit compared to the equivalent AV weapon.
For mitigators, I think a bigger GSP burn rate also makes sense. It might also be interesting to investigate whether modifying the breakthrough behavior (on both ends) makes sense - it would make sense for frontline air units embedded in a formation to be able to rapidly exploit the conditions leading to a breakthrough, but at the same time are more vulnerable to being caught with their pants down during refuel/rearm periods. Maybe something like 1. 25x breakthrough value and, say, double the cohesion damage (since they'll generally be suffering fewer casualties with the above mods)?