You're right. The story is a bit off. Looks like he might of paid up several days and no one bothered to do a morning door check for a few mornings.
Most motels I stay in do a morning door knock to check if towels or bedding need changing. The morning check also serves to protect the motel from scenes like this. No one really cares if a guy uses his laptop for an evening wank or whatever. A stench like this, though, being not only bad for business also completely ruins the room. It must have new carpets, bed, drapes and even need new paint or wallpaper.
Notice the pillow and towel condition. He must of just gotten out of the shower and was leaning over his laptop. Compressed heart and lungs and he might of passed out and died slumped onto his pillow. If he had a weak heart then his poor posture might of triggered a failure in the heart. Drugs or alcohol might of contributed.
All in all, a really rotten way to go... no pun intended!

See, that's what I thought. He had a week or two stay and probably died on the first couple days of his stay, but he may have had a do not disturb sign on his door.
As for what's in the bag, fuck if I know. I thought it was intestines at first as well, but that makes zero sense. Onions? Who knows, weird ass situation.