When using

php vendor/mage2tv/magento-cache-clean/bin/generate-cache-clean-config.php

or

php vendor/mage2tv/magento-cache-clean/bin/generate-cache-clean-config.php path/to/magento

to generate var/cache-clean-config.json, the file needs to be regenerated every time a module or theme is added.
This could easily be automated by a small Magento module that regenerates the dump whenever a module or theme is added.