Thank you for playing! After making the game and playing it some myself, I also felt like the minions should auto-aim while player is using the flag! It sounds to me you were using the flag correctly! I'm even thinking of making a shield or something for the character because I took some bullets for my minions in the same way too :D
The recall flag-without placing it sounds clever and the despawning of enemies sounds like a good idea for the bossfight. We tried to make some introduction to it, like spawn in players view with a big effect but the bossfight and the endgame in general is really rushed since time was running out.