TLDR: you can safely edit the clan settings.

Interesting. You're the first person to mention this and I haven't noticed it, but this could be a me thing. All my clans have a 2% chance to spawn, but also have a window of 1 - 1000 days, while the base bandit groups have small windows (like day 7 - day 9). So on days where there are no other groups available to spawn, there is a 100% chance one of my groups will spawn when the spawning mechanic activates.

It sounds like my theory that if friendly/companion is checked they always spawn as friendly and never hostile is correct though. If you don't want friendly bandits, I would recommend modifying some of the clan settings, they will persist through the monthly updates, but the bandits themselves will still get a monthly refresh unless you save them locally.

I subscribed all integration mods. So idk if this is a bug of every integration mod you've made or base mod bug, but I notice that after some ingame days, they spawning with high rate and chances, like much more than zeds and things goes anarchy. Every friendly group just start searching for enemies and wiping out every zed or hostile groups. And after that everything goes kinda boring seeing such activities.