Currently, we have the plugin menu disabled for everyone but the Super Admins. This is causing the items in metaboxes.php to not display for anyone not a Super Admin.
I see you are applying the check to see if the user editing can activate_plugins with the apply_filters. If the plugin menu is not given to the Administrators of the multisites, the features are disabled.
Could a new release include the ability to have these options enabled, or toggled, from the Network Admin for instances where the plugin menu is not enabled? Also, any suggestions for a “quick” fix?