By using site set via config/sites/config.yaml

dependencies:

• venor/mypackagename or Backend Modul Sites Sets for this Site [dependencies]

it is recommend to unlcheck the clear-flags in the Advanced Options tab in BE TypoScript-module in order to prevent that the Site Set is overriden.

"If the website uses a mixed setup consisting of a TypoScript template (sys_template) and site sets, it is important to uncheck the "Clear" flag for constants and setup in the TypoScript template. If the "Clear" flag is checked (default), TypoScript settings from site sets are cleared and do therefore not apply."

refer to https://docs.typo3.org/m/typo3/reference-coreapi/main/en-us/ApiOverview/SiteHandling/SiteSets.html#site-sets-typoscript

You may deactivate the whole template record, but don't forget to include ts from extension via dependencies in your config.yaml. Notice than up to now not all ext. are site set ready, so this way could cause problems.