WooCommerce Tax Exempt provides you a proper system through which you can give tax exemption to selected customers and user roles.
You can enable a customizable tax exemption form on My Account page to let customers submit the required files and other information to claim tax exemption. The store admin can review the submitted info and reject or grant the tax exemption requests from backoffice.
Once the tax exemption is granted, a checkbox is displayed on the checkout page to let customers claim the tax exemption. The tax exemption details are displayed in order detail pages.
The store admin can also tax-exempt selected customers from BackOffice. These exempted customers may or may not upload any tax information but still, they will be able to claim the tax exemption just like the other customers who have uploaded the tax files and claimed tax exemption.