> Clearly though they are fine with charging a yearly fee to access the store. So why not just charge for the app in the EU IF that really is the problem here
Alternative app stores have to pay the CTF for every install starting from the very first one. Apps distributed in alternative app stores have to pay the CTF for every install after the first 1m.
The CTF is an annual fee.
In this instance, the app store developer is the same as the app developer, so the yearly fee for the store is being used to cover both sets of fees.