You likely won't feel anything amiss in the ride.
Another question is whether the brake bridge and seatstays are centered to the plane of the frame in that location. Not difficult to check, but if they're not completely centered, and the wheel is running in plane, then ignore it. The brake will work just fine, and once it's got a little dirt on it no one will be any the wiser.
But... if it's really bothering you, you can take a file to the NDS dropout and VERY carefully and SLOWLY bring that side up the couple .0001's of an inch that it'll take to get it centered.
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