I had a similar issue with my hub motor, although not as acute. When fitted to the fork, there was hardly any hub cover clearance on one side. Taking a closer look I found that there was a bushing on each side of the axle. These bushings fit down inside the hub cover where they seat against the axle shoulder. The purpose of the bushings, are to transfer the pressure of the fork nut down through the hub cover and onto the axle shoulder. The clearance problem stemmed from the fact that the bushings were not of equal length. I made a new bushing to match the other and it lined up great.
You may be able to rectify the problem with a new, or perhaps two, new axle bushings. If the axle is truly offset, your bushing will have to be made different lengths to compensate.
Before you measure for new bushings, make sure the hub cover is completely relaxed and seated properly to the motor casing. Make sure it is not binding on the axle bearing and holding the cover out slightly. I ran into this when reseating one of my covers. All the screws were tightened in an alternating fashion and it looked good, when I heard a loud pop. The cover was binding on the axle bearing and suddenly released. To check this, you could use a rubber mallet to carefully tap the edge of the housing (where the axle exits) and see if it gives way a bit. You could also loosen all the screws on the cover and see if a gap appears somewhere on the perimeter of the cover, indicating that the cover is not seated properly.
If you do make new bushing(s), be sure the faces are cut as square as possible.
Andy