If the site is not registered, it should be using the Free plan and have the same limitations. If not, you've found a nasty bug .
There are some exceptions to this rule, though. For example, sites that are hosted using MoodleCloud are always Premium, even if they are not registered in the Apps Portal. Check out which plan each site is on, and if the limitations don't correspond with the plan, then it is an issue.
You should always be able to see information about this in the Site Subscription page. I forgot to mention that you can only see the disabled features if you're logged in as an admin, keep that in mind. But you'll always be able to see the subscription tier and you can check the limitations for each tier at apps.moodle.com.