The limitations mostly come from using any client boxes on a SWM network with two Genies. The few that have two indicated it was something with the software related to whole-home viewing issues.
Rather than invest in fixing the software, to date, DirecTV just decided to limit customers to one.
That could be a decision based on software development costs, or related to hardware/installation/training costs - or even both.
As for hardware, a SWM16 would work fine. In fact today you could isolate one Genie using a BSF and it would work fine, but is not an ideal setup as it would limit whole-home playback.
There would never be a need for two dishes - you can use two SWM8's and have isolated networks, or just isolate one branch of the swm16. Better yet, DirecTV could make some adjustments to the software to handle multiple Genies, just like it handles multiple HR2x. If they fix the software, than most customers would still be ok with a SWM16.