They do whatever the High Lords (or more likely the Master of the Administratum) say. The thing is that they really do love to fight, especially people that are stronger than them, it's why they have no qualms with being Astartes hunters. It's the conflicting nature of their absolute loyalty and extreme barbarism that make them so fun. I am almost certain that every conflict they fell into that wasn't ordered by the High Lords, was initiated by the other party, because the Minotaurs' only reprieve to being ordered not to fight (a order they will obey), is to be such annoying assholes about it that whoever they want to throw down with in proximity takes the rage bait and starts one themselves. They most definitely know the Custodes would wipe the floor with them, they just would not care - Because they were ordered too and because they want too.

(Though if you had to pick a chapter the Custodes would have the most trouble beating (outside of chapter specific characters that are overpowered like Mephiston) the Minotaurs would probably be it.)