My best attempt at a minimum score run.
Corneria - 1 Hit - Fighting either boss is fine. You just have to wait out the timer until the boss is worth 1 hit
Meteo - 0 Hit - Going through the warp means no boss
Katina - 0 Hit - Just waiting out the timer until the stage ends. Fortuna would also work since it's on a timer, too.
Sector X - 0 Hit - Another warp with no boss
Sector Z - 5 Hit - I assumed that 0 Hit would be the best you could do on this level, but that's practically impossible without understanding how enemy ships decide to start following teammates. It seems completely RNG based, and I don't know if it's possible to manipulate every enemy to not follow a teammate at some point. Now why does this matter? Because if your teammate is being followed, then they won't pursue a missile or destroy it. So I have to kill the enemies tailing them to free them up. Each teammate will only destroy 1 missile before returning to the center of the level, so you need all 3 alive and free in order to take down the final set of 3 missiles.
Sector Z - 0 Hit - Just let your teammates do their own thing and have the enemy tailing you destroy the missiles. Thanks to t3h_Icy for pointing this out
Area 6 - 1 Hit - Just waiting out the boss timer until it drops to 1 hit
Venom 2 - 14 Hit - In theory, 0 hits on Team Wolfen should be possible. There are voice lines for when a teammate takes out the final member of the fight, but for whatever reason my teammates would not shoot at the final enemy. So I have to wait out the timer until the final enemy drops to 1 Hit. Team Wolfen also passes right through terrain and columns, so you can't get them to explode themselves. For Andross, you have to wait out the timer on the 1st face phase in order to drop him down to 1 Hit on the brain phase. The eyes are worth 6 points a piece with no known way to reduce it, and even having the eyes shoot each other or ramming them will still give you full points.
Total Score - 16 points
This score is so low that it doesn't even register on the final ranking screen because my verification movie dropped the lowest score from the screen (which was 10 points) to unlock Expert mode, otherwise it would have replaced the #10 ranked spot. I would have to re-do this movie on Normal mode as a first playthrough in order to save my score.... WHICH... might be the secret to having a teammate kill the final member of Team Wolfen which would net you 0 points and a final score of 15. Maybe next year : )
InputEvelution: This was an interesting run to watch! As someone not very familiar with Star Fox or even rail shooters in general, it was fun seeing a movie go in the opposite direction to what I'd expect by instead avoiding shooting as much as possible, even if it means flying in circles for minutes on end waiting for a boss to weaken itself before landing the final blow. Accepting to Alternative!