If someone stopped by, maybe she put the dogs in the basement because they bark/jump all over/get very excited when visitors are in the house? If that is the case, then maybe someone came by after her run, or followed her to the house and knocked on the door? Seems like in a small town people are more trusting of others. If could explain why everything except her phone was still there. You would think there would be evidence at the house though if something happened to her at that location and if she was talked into going in the car with someone, you would think she would grab her glasses or wallet. But a forceful situation at the house likely would leave evidence of that somewhere?
They have to have answers to many of these questions and just aren't putting info out. They would know if her running clothes were at the house. It was hot out so surely she would have been sweating and there would be some evidence of clothing that had been worked out in somewhere in the house.. bathroom floor, bedroom floor, in the laundry room or in a hamper. If she never returned from that run, they would likely not find anything like that in the house.
Has it been mentioned anywhere if she had a step father? I see mom, brothers, and the boyfriends family mentioned, but what about a step dad? I see her moms name is different than hers so assuming there is one or has been one at some point unless that is a maiden name?