I'm guessing this was a stop-gap measure until the new forging dies for vertical drop-outs were ready and the assembly process was ready to use the new parts.
I agree it's not a great solution and if it were my bike, I'd probably file the dropouts also.

+1 on the all the advice about replacing the axle. It should come out one side or the other and if one bearing surface is part of the axle you will need new cones. If the axle is just an axle, you should be able to re-use the existing cones. Be sure to check the threading and diameter of the axle, they are not all the same. You might also want to get some new lock nuts made for quick-release axles since they will have ridges on the face and have rounded edges to help the wheel stay in place and to make it easier to insert.