If you have the capability of crimping your own gadgeteer 10-pin connectors, you can make up a cable with the standard wiring at one end, and a “split/twist” connection at the other end similar to old floppy cables. You’ll need to cut the ribbon cable between connectors 3 and 4, and between 8 and 9. The two end pieces will pass straight through, but 4 and 8 will swap, 5 and 7 will swap, and 6 will remain 6. I suggest crimping the twisted end first so if you mess up you can try again, and put the untwisted connector on at the desired length.
And of course, make sure you leave pins 4, 6, and 8 (limit switches and multi-function pin) open at your encoder.
Added: Making the cable is definitely asymmetrical. However, once it is made, the cable itself is symmetrical in that either end can be at the encoder as long as the other is at the controller.