Hmm...
For Strike weapons, making them not hit enemy Fighters might be easy enough.
There's an old thing in the .WPN specifications, allowing for a Weapon to have a specific mask (see concept of a bitmask if you're not familiar with how that works) for evaluating collisions. I'm not sure if it's still working or Alex deprecated the code, however; I haven't messed with it in ages.
Essentially, you'd go into the .WPN / PROJ and write "pierceSet":["FIGHTER"]... I think?
I'll play around with this and see if it works. I wanted to write something to allow certain weapons to pierce through MissileAPI's reliably; I had a system in Vacuum, but it was a little clunky.