Are you speaking to me Jason ?
If so I'm not sure what the problem the OP is having. But I can say that "we" do not need to to any extra pin muxing with the 4.4.x kernels. We can just use sysfs to export the gpio's we need, then set direction, and value. *IF* all we need is gpio.
Some of the things I have noticed about universal io. First, you can only have one overlay loaded that uses any pins it seems. Secondly of all the overlays I've tried to use, non of them let you mux *everything*. So thirdly, what happens is that you have to attempt to use two overlays that somehow overlap, but do not mux the same pins. . . For our own purposes this seemed impossible. So, I had to craft my own overlay base on two different universal io overlays. Which I needed to use all the epwmss pins as pwm, then around 25 other pins for gpio. 6 inputs, the rest all outputs.
The overlay univ-all that Robert created based on one of Charles' universal io overlays seems to mux the most, and be useful. But again, for us, it wasn't perfect. Not a complaint, just an observation. This is why I *was* working on universal-io single pin mux files. But after discussing that with Charles, it sounds like that would not be very useful. For most people.
Now I *could* personally create a universal-io overlay that would allow users to mux *every_single_pin* the way they see fit. But would my effort be wasted ? I do not know . . .