Will I have issues with using two Y2 rails? The instructions explain the Y1 rail has no holes (page 26) and the Y2 rail has two holes drilled and tapped for the Bitrunner accessory. Both of the rails I received appear to be identical and have the holes for the bit runner.
The Y rails are the same for both sides. If there are holes it may be for the BitRunner on newer manufactured machines. The SO3 Standard machine had the controller mounted on the X rail back side. Maybe they are putting holes so you can mount your controller on the left Y rail as on XL and XXL machines. Did you get any drag cables?
Since the V notch goes to the outside and if all Y rails are drilled for the BitRunner it would make sense to drill all of the Y rails from a manufacturing perspective so you dont have to have different rails for assembly and shipping simplification.