I am not aware of any non-faction specific scenarios with such requirements for participants, and faction scenarios are just private WSs held specifically by and for a faction to promote teamwork and communication and all that. Some scenarios do prefer to reserve spots for members of specific faction types but that isn't terribly common since generally it is left up to players to decide what is reasonable and realistic for their own characters. Most of the time, public scenarios are open to anyone, regardless of affiliation.
Everything else is just roleplaying, so if a WS mentions that you'll need to be working with a specific local government or fighting a specific group, that just pertains to that scenario and does not require any sort of affiliation shift within the Combine itself.