1 The basic plan is for one app. I think they mean that you can create an unlimited amount of apps for that price but with those limitations.
2 That pricing is per app. If you want to have unlimitied apps you pay per month a certain amount plus an amount per user.
3 Free apps stay free. But you could upgrade those to take advantage of the backups etc that you have for paid apps. But then the app is no longer free but a paid one.
And indeed you can contact Mendix support for any furhter details. They probably assign you a customer support manager to help you decide the best option for you.
You can contact mendix support and get a clarification for all you questions and doubts regarding pricing and licensing.