The one and only time I've changed a motorcycle tire myself, I balanced it using the axle, but not on the bike. I supported both ends on speaker cabinets. I have had no issues with balance of that tire, even up to highway speeds.
If you're in doubt as to whether there's too much drag using the axle, I would suggest adding a little weight (maybe a 0.25 oz weight) to the rim before you change the tire, and see if it's enough to make the tire spin on the axle. In other words, support both ends of the axle, and turn the tire until the added weight is at the 3:00 or 9:00 position, and let go. If the minimal weight is enough to make the tire spin until the weight is at the 6:00 position (or better yet, enough to make it go past 6:00 and then swing back, like a pendulum), the drag on the axle is probably not enough to affect your balancing.
All this comes with the caveat that you'd be taking the advice of someone who:
a) is not a motorcycle mechanic;
b) has minimal experience balancing tires; and
c) does not go over 75 miles on his motorcycle, so balance issues might not show up.
You learn something new every day if you're not careful.
If you think I won't understand it just because you have to explain it to me, maybe it was bullshit to begin with.