This is actually correct. If you offer two registration over time to enter two different lists/preferences, the second one must be confirmed otherwise anyone can change a subscriber profile just using his email.
If the system block the second attempt, it happens you cannot offer different subscriptions over time. anyway, if you don’t think to offer different subscription, users won’t subscribe twice or if they does not confirm the second subscription the first one stays active.
As you see there are many scenarios, this is way the plugin offers all those options.