Hi Paul
Even though you asked Zoran, I post a short answer ;) We did the upgrade from Moodle 4.1 (third party MFA-plugin) to Moodle 4.3 (Moodle MFA in core) - our users did not have to start from scratch. If you are planning on upgrading from the third party plugin to the core plugin, you might check https://github.com/catalyst/moodle-tool_mfa/issues/457 (a manual downgrade of the plugin version of mfa_factor_token in the Moodle DB was necessary in our case).
Best,
Samuel