I can't say exactly what goes into the logic for pre-placed installations (this is the setting determined by the Assymetric OPCOM module). My knowledge is based on shit-tons of observing but I know little, if anything about the actual code. @highhead or @SpyderBlack723 would be better suited to handle the logic for pre-placement.

What I can say on it, is this: The pre-placement of installations is pretty good! I can't say it will always choose locations with insurgents but for the most part, the logic is definitely decent. For instance, I've never seen them placed in blacklist areas.

And also bare in mind, the pre-placed setting is basically what I'm using now to get the Insurgency started. And this ties into your question about military logistics. Assymetric factions can only add new fighting groups with civ recruitment HQ's and actual physical civs present on the map. That's it. These are key in the insurgency growing/maintaining their strength.

I used to not allow pre-placed installations in the past, before Insurgency itself was slowed down to what we see in the mode today. And I'll be honest, without any on mission start it makes interrogating civs or finding Intel on dead bodies totally pointless. Insurgency currently has a random sleep for new installations to appear, which is set to 30-60 minutes after mission start. So if none are placed at the beginning, none will be on the map at all until 30-60 minutes have passed.

After 30-60 minutes, the new installation centers will be in enemy areas and will probably make a lot more sense to you. Fast forward for a little while in the SP editor and take a look if you're curious.

Note: And as it stands with the most recent 1.3.5 update, civ recruitment centers can only recruit 1 new group per hour each, for up to 5 hours, and there's a 50% chance the recruitment each hour will fail. Long story short, these installations are important to the Assymetric mode, not just in recruiting new groups, but also in the civs arming themselves (weapons depots) and IED's being placed (IED factories).

For civ hostility, you can use multiple civ placement modules and blacklist like you would the mil obj modules, but unfortunately, I don't think civ pop (where hostility is set) has a blacklist option. So at the moment, I don't think you can separate hostility amongst different civ factions (not a bad idea though!).