Looking at the routing of the Y axis stepper motors the wires go inside the X50 bottom rail to a female plug at the front of the machine. Would there be any issues in pulling the wires out of the Y rail so I don’t need to route them at the front of the table. Instead I would put holes under the stepper motors at the back and route them under the table. This would clean up the front of the machine and prevent catching things on the wires.
It won’t likely cause an issue, the cable assembly inside the rail must remain connected as it has 2 pins swapped around between the ends so it can’t be eliminated, as long as you remove the cable and keep it in the wiring between the controller and stepper it will work. I had mine set up this way for a few months prior to converting to Masso and replacing the stepper wiring with shielded cable.
In theory the the cable inside the rail provides some level of shielding from EMI/RFI that would be eliminated by removing the cable. You should route the cables to avoid spindle/router power cables to limit potential issues.
here is the Onefinity Wiring diagram that shows the necessary cable cross that Derek mentioned.
Note that stepper motor cables, just like all cables on a CNC machine, should be shielded.
If you want to make yourself longer stepper cables, this post lists what you need.