Exactly how well a VPN improves privacy is highly controversial to say the least. Quite a few would go as far to say not at all, although I believe it's a bit more nuanced.

But most importantly, Apple directing traffic to their VPN by default would be an unwise move on all levels. It would put them in a position to be able to scoop up data on users, regardless of intent. Not only would that be devastating for their reputation, it would actually harm user privacy. If a single company can directly capture almost every single packet flowing in and out of user devices, governments are bound to demand access to it without an option to refuse. Even in the most democratic countries, government agencies aren't known for their restraint when it comes to accessing user data.

> For (2), why is this the case? Apple mostly just needs to delete content from the Keychain for deleted apps and throw a wrench into some APIs used for fingerprinting

Wouldn't that break iCloud syncing? Besides, preventing turing complete programs from uniquely identifying users on real world devices is an unsolved problem for all I know. It's not as simple as disabling some APIs here and there.