You need to manually enable “Show CorePackages” through the settings XML file or the solution you provided. The option does exist in the settings XML file however it doesn’t display in the menu. The only reason I can think of that would point to this being intentional is the fact that a user might accidentally delete an important CorePackage.
The other settings for showing specific services (CoreGui and PluginGuiService) don’t matter when Show hidden objects in explorer is enabled, they will be shown even if their specific setting is false. It would make sense for the specific setting for CorePackages to have the same behavior with Show hidden objects in explorer enabled.
This is intentional, as it is a setting for internal use. However, there was a bug some time ago where the setting was missing a default value which caused it to be enabled arbitrarily on random machines, so some users who still had that enabled would see it. That should be fixed in the coming releases