That would seriously complicate things, if a customer was the holder of an exemption certificate. Also, a re-pricing nightmare if the tax rate changes.

Not really, the price of the good and the tax rate would still be calculated separately with the sum as the final price at the point of sale, so all it would take is ringing it up as a "no tax" sale as usual.  All I'm asking is why can't they just price it with tax at the shelf?  
And I've seen plenty of re-pricing "nightmares" handled like butter when they want to.  How many times I've gone to the store and 5 out of the 10 items I need have changed prices by a few cents overnight...  Besides, according to Michael, the Europeans have already figured this out, why can't we?