Sometimes it is difficult to parse what comes out of pathological liar's mouth. You are correct in pointing out that everything that MS has said about that night, should be treated with suspicion.
If there were any clues, LE either didn't find them, or ignored them. It is entirely plausible that someone else was in the house. If you take away MS's timeline, what's to say that while he was at work, someone came to the apartment and knocked on the door. Terri opens the door, and BAM! Of course I'm already starting to pick holes in that theory.
If you can come up with an alternate theory, I'd be willing to consider it.
If a "John Doe" hired perps who failed in their attempt to kill Jane Doe while John was at work, John may have arrived at home, found she was breathing, and disposed of (or rearranged) any evidence, before calling anyone.