1) While I agree there should be alternative stores on devices, entire portions of the DMA are unenforceable and plain english. A few of these were pointed out in the article but weren't followed up.
2) Apple can not deeply integrate into other browsers like it has with Webkit/Safari on iOS - The argument that they can just do the same integrations with all the other browsers to provide PWAs is fallacy and indicative of someone who doesn't know what that engineering effort is. They built the integration because they built both sides of the bridge to make it happen.
3) Are Apple being bullies? Yeah, for sure. But it's their device, their platform, and if the EU really wants to have a DMA, they need to create their own Apple, plain and simple. Apple should be barred from the EU if they can't comply with EU laws. But the EU laws need to be written in a way that holds weight and is enforceable. "Must provide alternative after 6 months of first service" isn't enforceable. If the decision is "Launch this but do it twice" or "Never launch this at all", never launch is going to win. And so, you all will never launch.
4) I get that having an app icon is all the rage but is it really that bad to just bookmark things? If you all want to avoid the Apple tax, provide a store that apple can present to the EU that allows for Apache Cordova PWA. I think the onus for this is on the EU. Not Apple. If there is such a store-front already (that's not used by pirates) I'm sure Apple would work with them to integrate for the EU market. A company shouldn't have to provide their own components to adhere to compliance requirements when their original offering was/is already accepted. If you want an alternative, go build one.
5) The article uses a lot of strong emotional language and straw-man arguments. Is it a bad move by Apple to remove PWA Home Dock capabilities? Yes. But what alternative could there be when they are forced to also provide that for 3rd-party browsers that they don't have the same integration with (because they didn't write the browser, the code, and integrating the same security controls could take years). The entire DMA is unrealistic, unenforceable, and would be unconstitutional in the US. It's not a companies job to provide alternative markets, fair or otherwise. It's the EU's. Built it. Force Apple to use it. That's how you win.