You could use any 4-wire cable/connector you want, as long as you're willing to hotwire certain points. This includes anything from micro-usb, 4 pin mini-xlr, rj11. Or even hardwire the two halves together with 4 unterminated wires.
That said, I don't see much difference between using trrs and other connectors, other than what MOZ pointed out about availability of the specific jacks used by the ergodox.
Its not impossible to use panel mounted mini-xlr jacks if you wish to; just wire it internally to the right pins. But other than micro-usb, most of the other connectors use a larger profile, and rj11 while easily available ready made, are imo harder to make as a hobbyist to get custom lengths.
I personally like mini-xlr alot due to making audio cables with them, but they have a much larger footprint in terms of general size to fit into the ergodox case, and also stick out alot more than most aftermarket trrs plugs.
Or you could simply buy a pair of male+female 4 pin mini-xlr, and hardwire each connector to the pcbs, and connect them in between. As long as you use decent wires, pretty much any of the options will last.