Unless the EU makes Apple get rid of the yearly cost per installation, any app store other than Apple's is limited by the inability to have free or freemium apps, giving them a substantial disadvantage in comparison.
I think this would need new legislation that would push software regulations further than they've been before.
Apple can allow apps to be installed outside their app store. The fee they are charging is likely related to accessing their APIs and tools for developing iOS apps. Apple would have to be forced to make these free.
Currently you could considerably make an iOS app without apple's tools and APIs. But it would require significant effort to develope/reverse engineer these tools to make the app. Effort that is outside of the scope of most modern app development.
To force apple to make the APIs and tools open would likely require additional legislation. Saying not only must the device allow third party distribution of apps, but apple must support these activities for free. This is significantly different from making apple allow third party apps. It puts on them a real cost (not potential loss like allowing third party app stores).
This isn't a problem for other systems because they actively invite people to develop and distribute their software for their system. But it would have implications for game consoles. Sony, MS and Nintendo would have to allow any potential developer access to their tools for free with little obligation.
Apple is just being greedy and tries to disincentivise developers from using third party stores. They are not incurring any cost associated with those downloads.
They do incur the cost of the tools and APIs. They would argue they eat the loss to support their market place.
I would argue apple making their APIs and tools open for everyone is in their best interests. It's easier to control security issues if everyone uses the same tools and apis. But apple won't care as much.
If a third party app store provides a tool or service to improve their app store, should apple expect to be able to use that for free? Negating any benefit that third party would get for developing such an improvement.
If a third party app store provides a tool or service to improve their app store, should apple expect to be able to use that for free? Negating any benefit that third party would get for developing such an improvement
Sideloaded apps aren't asking for benefits from being in Apple's app store. They're asking to be allowed to exist on Apple's platform without being fined for it.
Apple has used other platform API and tooling at no added cost the same way everyone everyone else does. iTunes and Safari used to run on Windows. Apple provides AppleTV+ apps for several platforms. And there's a number of apps they make for Android.
Apple already charges developers for access to their APIs and tooling. What Apple is doing with the per-install cost is trying to charge developers for access to their audience — which is not what the EU intended.
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.