I think you'd be hard pressed to find many ZIP+4's that have tax district lines splitting it in two.  No large dataset is going to be 100% perfect, of course, but ZIP+4 is pretty damn specific.  And likely to be more accurate than even brick & mortal store sales tax application is now.

As for the actual remittance of the tax collected, yes, we never got to talking about that part.  That may also be a function appropriate for a federal service -- a clearinghouse "bank" of sorts.  That way a retailer could just send it all to one place to credit the multiple tax districts, and those tax districts around the country collect their money from there.  That could actually be more efficient than what they do now (sending it multiple places), saving money for them.  The federal clearinghouse could either be funded through a small participating retailer fee, or participating tax district fee, or both.  And it doesn't need to be some huge federal bureaucracy, just a fairly basic clearinghouse.