They are charging a development fee. Then a per user deployment fee for each copy of the software distributed. This is a normal structure for many commercial software.

You can still develop an iOS app and deploy it on a third party iOS store. It just can use any software that apple charges for.

The EU would need further legislation to stop apple from doing this. It would also have to be targeted very particularly at apple, else software licensing wouldn't work.

To tell apple they couldn't do this would require invalidating copyright licensing for all software generated by an OS provider that can be used on a application.

In all the examples you've suggested the software was given freely from the OS providers to apple. They didn't ask for any money. Largely because they wanted people to make software for their systems. Video game consoles do exactly what apple is doing. Further they even have means to restrict the content that you can publish at all.