Just because Apple sets the rules doesn't mean they are not anti-competitive. Hence the EU's decision to investigate the situation. Apple will have to justify treating digital goods differently than other services or physical goods; something that I personally don't believe and that you can't rationally justify either (and no, their store their rulez is not rational).
Actually, the issue of digital versus physical goods and services won't be an issue before the EU as no one disputes that Apple has the right to not be involved in those areas. Otherwise, the EU would be considering whether Apple should be forced to charge Uber, Amazon, etc., for the physical goods and services that are sold through their Apps.
The actual issue raised, improperly IMO, by Spotify is whether Apple can build a store and then sell a product in it as a lesser price than its competitors? If Apple didn't sell Apple Music, then this particular issue wouldn't be before the EU.
Lastly, when you claim it is ""for a company to be able set the rules for the products that are sold in their stores, you do realize that is exactly how it is done and has been done for most of humanity? You may not agree with it, but that is the essence of capitalism and free markets. If you and I get together today with a group of venture capitalists and decide to offer a music streaming business with an App, we don't get to tell Google and Apple what they get to charge us to use their App stores, any more than we get to dictate to Macrumors to use their site to advertise.