> iOS apps distributed from the App Store and/or an alternative app marketplace will pay €0.50 for each first annual install per year over a 1 million threshold.
>Developers can choose to adopt these new business terms, or stay on Apple’s existing terms. Developers must adopt the new business terms for EU apps to use the new capabilities for alternative distribution or alternative payment processing.
You don’t have to pay the fee if you stay on the existing business terms.
> Also today, Apple is sharing new business terms available for developers’ apps in the European Union. Developers can choose to adopt these new business terms, or stay on Apple’s existing terms.
Nothing here suggests the new terms replace the existing terms, just that it's now a choice for developers in the EU.
> iOS apps distributed from the App Store and/or an alternative app marketplace will pay €0.50 for each first annual install per year over a 1 million threshold.
So App Store or not, you need to pay the fee.