I just put an encoder in each of my panels, and then run a single USB out to the cabinet. This isn't the cheapest way to go, but it's damn simple to make new boards, and gives you some flexibility. If you're using something like the Zero Delays or Xin-MO boards, then it's not much more than the cost of molex connectors... and much easier.
On the Pi though, I have to restart to use the new board. Which kinda sucks. On the PC side, I haven't had to do that.
The added benefit of the onboard encoders is that you can use them on other machines (if they fit). I have 4 machines here in the basement that are all interchangeable. I use a variety of encoders... zero delays, ultimarc, GGG.