While doing our testing when updating from Matomo core 3.14.0 or older Matomo won't update the Provider and custom variables plugin. There's no real possible workaround because we can't change the update process so figured the best and only workaround be to continue shipping the plugins for a while with Matomo see https://github.com/matomo-org/matomo-package/pull/112 . The plugins won't be updated because Matomo thinks the plugins are bundled with core in https://github.com/matomo-org/matomo/blob/3.14.1-b1/plugins/Marketplace/Api/Client.php#L170 (could think about removing that check in the future however would make the post request a lot larger and put bit more load on the marketplace potentially but nothing serious I suppose)
When people then upgrade from older Matomo versions to a newer Matomo 4.X version without the Provider and Custom Variables plugin, this change will make sure that the marketplace will look for updates and find them. By adding the plugin.json the plugins will be no longer bogus.
What is still a problem is that when updating from a version before Matomo core 3.14.1 is that the 2 plugins will be deactivated. There's no real workaround since we can't know whether they were activated previously. What happens is that a user eg updates from Matomo 3.10 to Matomo 4.8 (the 2 plugins are no longer shipped with Matomo):
Without this change Matomo would never even show there is an update for the plugins available.