Many AvaTax integrations provide a way to not send over transaction data for specific invoices, customers, states, etc. The method of filtering depends on the integration. So, it is possible to have AvaTax not calculate when you do not need it to. This can have unintentional results.
Sending non-taxable transaction data to AvaTax still has value. Many states, like California, require you list your gross sales, and not just in that state, but everywhere in the US. So, providing the non-taxable/exempt data to Avatax can be valuable, since without it, our reports will be incomplete. Being able to use our reports, or our filing service, as your primary source of data for filings can simplify the filing process.