It's interesting to contemplate how low-scale PvP (banditry, mercenaries, etc.) can be made viable without consistently escalating into Settlement-level conflict. That is, I'm hopeful that players would be able to play as Bandits and Mercenaries and not automatically call down the wrath of their victims' Settlements on their own Settlements. I'm not sure how to make that happen mechanically - maybe it just has to be that we decide as a community to "look the other way".

I'd suggest that there needs to be a place for mercenaries in settlement-level conflict. I think that in private wars between companies - feuds - the mercenary is either a hired killer (taking rep losses outside of the company) or a ringer (inserted into the company as a member, though he really has no affiliation*). I think company alliances/defensive pacts as suggested by the OP should be long-term attachments that other companies can take into consideration during their planning.

* I don't think company hopping should be prohibited, just as I don't thing PvP outside of 'sanctioned' methods should be prohibited. There just needs to be enough downside to make it a real decision; sometimes the lesser evil of choices.
At some point, crowdforging suggestions seem to be like fan fiction. Some good, some bad, some repetitious and predictable. But maybe there are some gems out there.