Thunderbird can be customized by organizations via policies, see https://support.mozilla.org/en-US/products/firefox-enterprise/policies-customization-enterprise/policies-overview-enterprise.

Add-ons can add support to be configurable via the same mechanism, see https://extensionworkshop.com/documentation/enterprise/adding-policy-support-to-your-extension/ (at least in Firefox, not yet tested in Thunderbird).

The add-on should allow to set the default values for the non account specific options.
Optionally also allow to lock the settings.

See #267 for a workaround using about:config and autoconfig until this is implemented.