it's meant for you to use ur crew as boarding party , it's more of a PvP thing as you can give them grappling hook after ur Harpoon on them, as have them reelin' you to them, if your NPC have grappling hooks they can board other player ships with you and basically have your own army. Also Red alert is also "abandon" ship feature so you can dismount them all and whistle them to follow you as you swim to safety/to invade.
To use it effectively you need think outside the box when using it, other then that it might be a life saving to dying moment if done wrong.
Hope While TV shows have change what Red Alert meant long time ago to having a lot of meaning now, but then it was basically way for people to save their life to live one more day maybe, cause back then it was a fight or flight thing when a ship was sinking,
This is why if u try Red alert while "dock" u might have all your crew run off the ship, it basically the "Eject"
As for getting to stop shooting while in red alert, put them passive. You'll notice they'll generally not fire in passive mode
