If the 0.00001 grams of the magnet is off-balancing your wheel, there may be a bigger problem with it. I’ve got the little magnet on my front wheel, and it doesn’t send me tumbling when I’m over 30-35 mph, so I’m fairly certain it’s a total non-issue.
As far as the calibration issue goes, honestly the computers are guessing to the best of their abilities based on outer diameter assuming a standard inflation rate. GPS’s are highly sophisticated systems based on satellites. My navigation GPS and the speedos in my cars don’t always get along. Mechanical vs. satellite. Really, it comes down to how accurate does it really need to be? I’ve checked my bikeputer vs. MapMyRide vs. a Garmin mounted on the bars. Honestly they’re so similar it doesn’t matter that much to me.