Personally, I hope they leave certain locations in the game un-Clear-able, it's always fun to go back and fight more Raiders. However, after a second trip to the area, after some time had passed, enemies had respawned and I got to kill all the Raiders again, this time, however, the map told me it was 'Cleared.' I ran through the Corvega Assembly Plant, killed the final 'boss,' Jared, and my map never told me it was Cleared. Killing the final boss, as others have stated, would make sense, except that it doesn't seem to hold completely true. I am wondering if there are one or two left over somewhere, the area may not stay clear. As soon as I spawned in I got a Molotov to the face! I dropped into the ironworks today and was attached by the forged who I killed on a story mission. It's also ANNOYING because it's clears on the map and is presumed safe. It would be nice if areas remained clear as it really ruins immersion when you have played a part of the story where you have to clear an area and you fast travel there later and the people are back. Some places that don't have a boss like the supermarket still read as clear when most enemy's are dead or wounded. Not all enemy's need to be dead for the area to be clear which is misleading as I have been tricked by that before (false sense of security). I have found if your on a mission or not, after killing most enemy's, the area will show as cleared on the map.

I have cleared areas on missions and also just by stumbling into them and exploring.

Fallout 4 ares mod