I don’t think your missing something. This is Apple’s way of discouraging use of an alternative app store for popular apps, or alternatively, of encouraging subscription models.

> Core Technology Fee — iOS apps distributed from the App Store and/or an alternative app marketplace will pay €0.50 for each first annual install

emphasis added on and/or; it seems like Apple is being forced to break down fees according roughly to their costs (?). Maybe installs from altapp stores cost them some resources because they want to verify the notarization each time?

Apps don’t have to pay for notarization on MacOS, and nobody forces Apple to perform notarization in the first place. It’s also implausible that there would be any notable cost per install.

That is the point. This is malicious compliance, presumably they expect to get away with it while the legislative/legal systems in the EU spend years grinding through the process of figuring out how to punish Apple for it.