Avatax Exemption Codes/Certificates (CertCaputure) allow you to mark customers as non-taxable (eg. E = Charity) and/or, using certificates, set specific tax rates eg. 2.5% for farmers.
The "Exemption Certificate No" is located on the customer record/Avatax tab in NetSuite. If this field is populated, the "Taxable" flag is not used. If the customer in NetSuite does not exist in Avatax and this field is set, Non Taxable is used. If the customer does exist, that particular tax rule is applied.
The Avatax Configuration for the Customer Code must be set to "Customer Internal Id". When creating/importing the customer in Avatax, the customer must be set the the InternalId of the customer in NetSuite in order for the customers to correctly map.
In NetSuite, these exemptions/certificates are entered into an AvaTax custom field ("Exemption Certificate No") and when NetSuite uses the Avatax tax engine, this field (not the "Taxable" flag) determines if a customer is taxable or not. In NetSuite (without Avatax), "Exemption Certificate No" is not supported and therefore no consideration is given. SuitePOS in that case only uses the 'Taxable" field.