once you have cleared an outpost/checkpoint (provided its not a a future mission) it stays cleared for the rest of the game. so if you clear all the check points from the game, then you end up with no enemies left to fight outside of a couple mini games and a certain side quests.
Cool. So it actually makes the player feel like they are making a difference on the island.
Whats nice is if you want to keep the level of difficulty higher you can leave the camps alone. Camps only provide a few side quests such as Kill or Hunting. So by leaving them alone you're not really hurting your advancement while keeping the islands occupied with enemy forces. It should be noted those hunting quests can be for rare skins used in making the final tier of an item.
Speaking of which, its fun to take on a group that are patrolling a road. Typically when you do so, no matter how quiet you are additional reinforcements arrive quickly. While not difficult, it does to the enjoyment of the game.