You're right. For multisite, the settings page should be put in the network admin instead of each site's admin and the license key should be stored in the network options. I didn't think about this at first. Let me try to update the plugin.
PS: Just updated the plugin to support multisite. In Multisite environment, the settings page is moved to Network > Settings > Meta Box Updater. Normal site admins won't see the message and that settings page. Please update and let me know how it goes.
PS2: Your license for Core extension bundle is expired. Please update to get updates for other plugins.
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