Does autohop work OTA? Regardless, even if it didn't, they're not measuring eyes on a given commercial. They're measuring eyes in 15 minute increments at best. So for those that have Nielsen sensors in their home (vs filling out the book), If you're watching a show at 6:01, it's assumed you're watching from 6:00-6:15. I think those times are right.
And going back to the argument this always comes back to, who gets to consider what's "fair"? Presumably ALL MVPDs are ok with paying locals, otherwise retrans would never happen. Presumably MVPDs are fine paying whatever the past rate is. Again, Dish (any MVPD) has the power to say "nope, that's too much money, we're not carrying you."
At the same time, I do think broadcasters can be asking for too much. I don't know that I could even tell you how much "too much" is. At least with Dish, customers have the option of not paying for locals.