I cannot even begin to tell you how many times I have had to steam clean stains out of the carpet from my kids when all the usual carpet cleaners fail. I think if there is truth to the fact that a large stain was found, they are either certain it's not your typical stain and are thinking it could be bodily fluids/feces or they aren't sure and are just being thorough in their investigation. I also wonder if they sprayed luminol and found parts of the stain that tested positive for blood.
I remember in the CA case they tested the trunk and Dr. Vass from the body farm testified that there were certain compounds present directly resulting from the human decomposition process, so maybe they are going to test for that. I know its a long shot but who knows how certain cases are handled after that high profile case.
If a stain was caused from the body's purging and/or decomp process, I would think there would be an odor, unless maybe there was a bunch of bleach used in one area that was obvious to investigators, or maybe there was blood in the stain that they found if they used luminol in the apartment?