If we take the two Eddie alerts inside the apartment as primary can you see that they are compatible with a scenario in which both parents and group are completely uninvolved. These two alerts could be the direct result of actions of a stranger intruder in the apartment. Why not investigate these alerts in that light? Obviously given that one of the alerts was at a shelf where a pile of clothes was stored during that meal, it would directly explain the clothing alerts too. That leaves only the vehicle alert which would be secondary transfer from those clothes.
There are two difficulties of tying what you suggest in with Eddie's alert.
The first is that if an intruder killed Madeleine in the apartment and took her body, there would be no time for accumulation of a death scent inside the apartment.
And the second is that if an intruder killed Madeleine inside the apartment and left her body there, who found her body? ....
I honestly don't see either being right.