Because in both cases there was no testimony, direct evidence or claims that the crime occured within the home. Everyone may suspect it, but LE would have to have some degree of proof to declare it an official crime scene,and take control.
This is similar to the Caylee Anthony case, where since the initial assumption was the crime had occured after the daughter and grandaughter had departed the grandparents home, that house was not considered an official "crime scene" just a source of evidence, until much later.
In the case of Hayleigh, the claim from the begining is that the home was broken into and the girl abducted from her bed. That makes the house the scene of a crime from the word go, and the initial scene of a crime in progress (if it is an abduction). And LE can act as they have.
I was just wondering about the Elizabeth Smart case. Did they keep the Smart family out of their home for so long? I can't remember.