With DirecTV you can use any DVR as your main MRV Server (Hopper) and any as a secondary device (Joey), and it is the same price regardless. No matter the setup you have an extra receiver fee which is the same for all additional units regardless of the type and the number of tuners, one flat DVR fee, and one flat MRV fee. All of this is irregardless of which receiver/DVRs one is using (one tuner or 5 tuners). Dish can easily do the same.
One complaint with D*'s MRV is that there is no central control/viewing of the series manager and todo list. Makes it a PITA to manage recording series, not a major PITA that makes you want to throw a remote, but a PITA never the less. You get that because of exactly what you are describing. Of course, the advantage of the D* system is there isn't a central point of failure also.
With E* and one Hopper, everything is done on the Hopper. Either by the remote talking to the Hopper, or via the Joey being controlled. And assuming that a 2nd Hopper at some point will be fully integrated, you still have central management. That is a big plus for the Hopper/Joey design. The downside of a single Hopper install is you have a single point of failure.
BTW, with D*s design, and using RVU TVs or the rumored upcoming RVU box and an HR34, the system is essentially the same as the Hopper/Joey install with the same benefits and downsides. When/if D* gets the RVU box out, and/or more TVs show up with RVU, I think you'll see D* pushing for a similar install to the Hopper/Joey. Makes financial sense for the company side. Reduces cost of the install.