I think the problem/perception is best illustrated when you compare quest and non-quest POI's. If I clean out "Al's Fish House" and it's
not quest-associated, then I'm forced to wait a period before I can return and clean it out again. Some loot won't be there on the 2nd clearing, and any resources harvested (plastic from blinds, etc.) also won't be there.
With a quest POI you can double-dip, but really only on the first run....so it's not that big of an issue (it may feel like it).
A bigger problem would be that you can run through a quest, grab all the loot, but leave a few zombies alive. Restart the game and voila!....repeat as many times as you feel like. Need books?....you can clean out all the shelves of the bookstore over and over and over.
Who's to say what should be part of a SP experience, but I feel that you should FAIL a quest when logging out. We'll occasionally get burned by lockups, power-failures, crazy dogs, etc.
-Arch Necromancer Morloc