You want to use the Partner Internal Id as the Customer Code. However, when creating invoices the Customer Internal Id is passed to the Admin Console as the Customer Code.
To use the Partner Internal Id details during tax calls, you will need to uncheck 'Multi-Partner Management' option in NetSuite (Setup > Company > Enable Features > Company > Partners).
If this option is enabled, while creating transaction, Avalara does not get Partner (Header level field) value even if Partner is selected at line level under Partner Tab.
The above same condition is also applied for Customer master where Avalara uses Partner details for CertCapture functionality.