Thanks for the update @swinggraphics. There is a banner that does appear upon deactivating and then re-activating the plugin. This banner is a notification that the plugin has been activated. See below:
I’ve made a recording of the expected behavior here, which shows some non default settings applied within Site Kit. After deactivating and then re-activating Site Kit these default settings remain intact.
As what may be occurring on your test sites sounds unusual, would it be possible for you to share a screen recording and we can check this further? It’s possible there may be third party plugins impacting the standard behavior. You can use a service such as recordit or jumpshare to share a screen recording, while using this form to share privately if preferred.
It may also be possible that your SALT keys are changed, another admin has made changes, or your site URLs have changed, which may impact how a plugin deactivation works, which would result in a different banner upon reactivating. Once we can see what’s occurring we can check this further. Thank you!