Over the years I've seen more than a few bikes with offset front wheels, so it's not something new. Ideally I would want my front and rear wheels to be perfectly aligned so the rear tracks exactly the same line as the front, but if the difference is very small it might not really matter. After all, often a totally stock Harley doesn't track perfectly straight either thanks to all their tolerance stack-ups.
As Twolane mentioned, the reason for your particular situation is likely due to the rotor mounting surface of the aftermarket wheel (I assume the bike has the stock legs and caliper). Verify that the rotor is centered in the caliper and not also shifted to one side. If it's centered properly in the caliper, before you modify anything you should determine the brand of wheel and consult with that company to see if they have a properly engineered solution to the issue. You may be able to center the wheel and then shim the caliper to align with the rotor, or perhaps shim the rotor to the wheel, but either way I'd want something better than just throwing a couple washers under each attachment point.
JMHO - Jerry