But how do we know that they didn't knock on the doors, ask the owners (if they were home) if they had noticed anything out of the ordinary, and then ask permission to look around the property?

My wife's cousin lives right outside of Boston and they had FBI and Massachusetts PD combing the area. An FBI agent knocked on their door, they answered, he asked if they knew what went on that afternoon (which they had and acknowledged they had). Then he asked if they had noticed anything suspicious or out of the ordinary in the neighborhood. They said they hadn't, but if they did they would call the Mass PD. The FBI agent said thank you and left.

I'm sure not every person involved in the man-hunt was as professional, but I do think that some of this stuff is overblown.