Just as the title says. At the main screen there is a check box for disabling the Pirate equipment but it is red and no matter what I cannot get rid of the Pirate gear/mechs.

Every time I have a mission that requires killing a certain amount of mechs and one of them fails to spawn, it's on a pirate mission where one of the broken pirate mechs fails to spawn in and I am stuck. Either from a Jump ship that is stuck hovering in place forever or they just fail to spawn in the map. This happens way too often and I want to get rid of them but the option isn't working.

Is it maybe caused by a mod conflict or is it just broken?

I don't particularly care for the broken balance they throw in game, nor care for facing up against an Annihilator equipped with 4 scrap cannons making it so I can't see anything.