"Uninstall" (migrate down) feature in Flarum only removes data that the extension added through database migrations, so it often doesn't include the settings which are stored in a Flarum database table.
For it to clear settings, the extension developers need to add a migration that inserts an initial value for settings, and clears them in the down function. Very few extensions actually do it, so in practice settings aren't impacted by that feature.
There's also no way for Flarum to automatically reset the settings because there isn't a standard naming or registration system for settings at the moment so Flarum has no way to know which setting value belongs to which extension.
