The Kroot are known to be exceptional hunters and trackers. They are also known to be extremely prideful. As such, not all of the kindreds have decided to accept the Imperium’s offer. Many of these clans also hold to their racial tenants a little more loosely than most, willing to consume any enemy they deem a worthy combatant, be they even Tau or Human. And many of these Kroot are willing to take assassination contracts if you can give them what they want.
Meeting these Kroot will not necessarily result in an immediate attack, but most will be aloof and ignore most non-Kroot who they deem not worthy of their time. They have no official power base and float amongst the stars in their battlespheres and possibly a few ships they have come to acquire over the years.