Of course Apple tracks its users. Every company tracks users that have paid for services from them. It’s the only way for them to actually provide those services. Creating a username/password is telling that service, “This is who I am, and when I come back, I want you to remember me. There are features of your service that you provide when I give you this way to track me that’s worth being tracked by you.” It only becomes a problem with a company that a user has NOT entered into an agreement with is tracking them. That’s Third-Party tracking.
Safari’s been pretty effective at throwing a wrench into third party ad networks ability to monetize Safari browser users. As a result, some companies that REALLY want that third party ad networks revenue are forcing users to use their apps. Because those apps tell the users what they’re going to track when they download them (in the App Store description), they end up having access to FAR more data than what they get from a user using Safari.