1. Apple creates iPod, and iTunes serves as its music store.
2. Apple creates iPhone, which has an iPod app.
3. Apple introduces App Store so other apps can be used on the iPhone.
4. iPod (Apple Music) competitors emerge.
5. EU says "that's it, Apple can't have iPod anymore on the phone unless iPod (Apple Music) becomes a separate company".
No one (successfully) sued Apple for anti-competitive practices on iPod. Ergo if the iPhone never had an App Store, they'd be allowed to have 100% of the revenue of iTunes, and ban competitors out completely.
By opening the iPhone platform to third parties, EU sees them as another type of entity completely. In effect the EU penalizes the creation of market places, because once you're market place, you lose control over your own products to the government.