As an engineer who has worked in both hardware and software development, IMO the reason they didn't allow VIP receivers on the Hopper system is to greatly simply testing and maintenance of current and new features. If they keep Hopper/Joey self contained, then they don't have to run test cases on every single combination of equipment out there. This task grows exponentially for each additional combination created. It also lets them handle VIP and Hopper as separate technologies and then they can make business decisions on each without having huge complications. i.e. "We can't add this feature here because it breaks this over there."
Since people, for the most part (exception for those on this forum), won't take any time at all to learn anything about their equipment, Dish has to assume that any change has to be easy enough so that a chimpanzee can handle it. (OK, maybe unfair to the chimpanzee) So they have to endlessly test any changes or they face what, I should imagine is a nightmare where they push out an update, and it takes 1000s if not tens of 1000s of systems off line. It's hugely complicated for systems as sophisticated as these. So from a technical perspective, I would say this is why they did it.
Not everyone, in fact I would guess that most of Dish's customers are not going to want a whole house DVR system as I'm sure there are many with just one TV and receiver and are not interested in anything else. At the end of the day, it isn't about the system but instead, its the content and Dish needs to maintain a very low cost option out there because ultimately they are competing against the local cable and telephone companies, which in a lot of areas still, offer a no set top box option and bundles with wired Internet and telephone. They won't want to add cost by making it compatible with Hopper.
