For what it's worth, we charge our county specific rate on all transactions for our state. At the end of our reporting period, we have a list of all transactions by zip code and we charge the exact rate then (not at the time of transaction). In an excel worksheet it's easy enough to use a table rate look up function.
As you discovered, the overall discrepancy is only fractions of pennies on the dollar. I'm sure there's accountants who would say this is a really jerry-rigged way of doing things. But the accountants who I've spoken with say they can't see the IRS having an issue with doing it this way (and why would they? at the end of the day they're getting exactly what they should be getting in revenues).