Everyone's "routine" is different, what makes sense for one person, another wouldn't do. I keep my dogs put away also, and while I usually let them out first thing, sometimes I don't. If I have groceries or something else I don't want them getting into, or if someone is coming in with me, they stay up until it's safe. She could have let someone she knew in with her when she came back from a run and kept the dogs in the basement thinking she would let them out when the person left.
But like you pointed out, the dogs were fed and in good condition and that makes me think something happened in the early morning. Just moo, all speculation, toss it in the speculation pile with everything else