I’m guessing this was a stupid question, based on a misunderstanding on my part about what the plugin is doing. I guess that the option to Activate appears against any user that has not been activated with the plugin, so that would include pre-existing users who signed up via the WP default method. Hopefully there is no impact on these existing users.
If anyone knows different, feel free to say. Meanwhile I am continuing to have these conversations with myself, in my head, but will stop this dialogue with myself on the forum as it’s becoming embarrassing.