@Mogreid I know your post is a few months old but I just encountered something quite similar during a campaign in the Georgia theater.
I joined the 71st as an escort flight out of Batumi A.B. , escorting a naval strike flight who’s target was…
Port Royal SAG (USS Port Royal and USS Momsen - US Navy!
A strange frag but OK - I’ll play.
My 2 ship gets waxed by missiles from the USS Port Royal.
In the end, the color-coded indicators of NATO, Russia etc. are completely arbitrary - you can have any “side” own any asset but it does kinda mess with the immersion for me to being flying for Georgia but fragged to attack what feels like a friendly.