If I have the AIO addon installed on a site, do I still have to individually install all of the other addons, or can I use the addons with only the AIO installed?
I've seen some threads by developers who are bundling CPTs into themes and other projects using Metabox. Does this mean there is a whitelabel option or a way to hide the MB menu item from within the WP Admin dashboard?
No, you can just use the AIO plugin. Just a note, if you need free extensions, they will be installed independently. AIO includes only premium extensions.
Yes, it's white-label partly. The main menu is requires for some extensions such as MB Custom Post Type and Meta Box Builder. But if you don't use them, and use only AIO, then you can filter the mb_aio_show_settings and it won't show the menu.