Can I use the usb power cable from the ATXRaspi to the raspberry pi to carry the data from the 2 gpio connections between the two boards?
The short answer is no.
How would you envision even doing that?
I was not sure if the pi and/or the ATX carried data on the USB data wires or if they were connected on the PCB's. If not, my thought was to jump the GPIO leads to the usb connector and do the same on the ATX.
I was looking for a solution to house the boards in different cases using only 1 cable connection
The Pi uUSB only carries power.
I guess you could jump if you want, that was my first thought but you'd put quite a bit of effort into that if you don't have a microscope.