Autohop kills the network commercials. Those are commercials ABC has sold advertisers that are guaranteed so much viewership (i.e. gross ratings points). Whether the commercials are being skipped on their owned stations or affiliates' stations it does not matter, they lose a viewer with every hopper. For them to settle the lawsuit you can bet they want revenue from every hopper, not just customers in their O&O markets.
If a station is in dispute and pulled off Dish, the commercials are not being autohopped....