Because "Ask App Not To Track" refers to (for all apps, not just the App Store) tracking across different systems/companies.
For example, a Weather app collaborating with an ad sales company to provide them tracking data would violate "Ask App Not To Track," but Facebook tracking you within the Facebook app does not because it's all internal.
The reason for this is just about the practicality of enforcement: You cannot enforce companies not doing internal tracking because they still have to collect data for their business, so how do you distinguish it.
For example, a Weather app collaborating with an ad sales company to provide them tracking data would violate "Ask App Not To Track," but Facebook tracking you within the Facebook app does not because it's all internal.
The reason for this is just about the practicality of enforcement: You cannot enforce companies not doing internal tracking because they still have to collect data for their business, so how do you distinguish it.