From the drawing it looks like the plan is to mount the rails on the top and bottom of the welded box section? If so you'll have problems with how much the steel will distort due to the welding. The rail spacing needs to be very accurate (guessing probably <0.05mm) for them to run smoothly, which is hard to get even before welding. Perhaps consider bolting them to a backing plate instead, since this allows adjustment to get the rails parallel. Also you will get much less deflection on this Y-axis if the ballscrew is placed between the rails. Currently when a force is applied parallel to Y, the Y-axis bearings can deflect in the same direction since there is a long horizontal distance (parallel to X) between the cutter and ballnut/rails.

If you decide to mount the rails on aluminium plate (as in post #15), then yes it is best to use tooling plate, but realistically the tolerances of the bearings are not that good so you would be fine with normal aluminium plate, but definitely not flat bar. If you were using profile rails then tooling plate would be the best option.