Hey!
Thanks for the questions. Combat should not be possible in a faction location unless it is the faction that that location belongs to. This is a problem I've been asked about before and need to include in the errata. You could treat this as a one-off combat encounter as well, your choice. It should be assumed that each hex is larger than just the location inside, so encountering Raiders is highly possible as they would be out-and-about doing their thing.
As the game stands, Raiders cannot take over faction locations. There are some unique rules in the game that will change faction ownership but never for the Raiders. It is briefly mentioned, in my scrapped ideas section of the game, that I wanted to include Raiders moving across the map and taking over locations but didn't include it.
Every time I revisit Courier I see another issue that I wish I could go back and resolve for the printed copies. :)
As always, let me know if you have any more questions.
- Cody