Since "FlaggedRevs" has been migrated to extension registration (extension.json), the value of $wgFlaggedRevsNamespaces can not be set properly in the LocalSettings.php.
FlaggedRevs sets NS_MAIN, NS_FILE and NS_TEMPLATE as default for $wgFlaggedRevsNamespaces[1]. Unfortunately as array_merge is used as a "merge strategy" for this setting by default, there is no way to remove any of these again.
e.g. setting
wfLoadExtension( 'FlaggedRevs' ); $wgFlaggedRevsNamespaces = [ NS_HELP ];
in the LocalSettings.php will result in $wgFlaggedRevsNamespaces === [ NS_MAIN, NS_FILE, NS_TEMPLATE, NS_HELP ] instead of $wgFlaggedRevsNamespaces === [ NS_HELP ] on runtime.
Therefore admins can not disable FlaggedRevs for NS_MAIN, NS_FILE or NS_TEMPLATE anymore.
Tested with
If any possible a fix of this should be backported to REL1_35 of this extension.