You can't automatically reset POIs in case someone has their base setup there.
The argument may then become don't reset if there's a base inside but then what does that mean? Is there a bedroll present? What if I have a horde base or outpost without a bedroll? There's too many edge cases and subjectivity around the matter imo. The current implementation, while not perfect, is the best option.
It also plays into the survival/ role play aspect to have to manually track progress. Leave some kind of marker outside so you know what's been looted. I use wood frames in the doorway - inexpensive and easy to identify on approach.