Hello Zeno, welcome to the forums!
Here’s the thread that @dotcoma mentioned about installing WhatsApp under Shelter.
To clarify on why Apps from the default store are not modified and may contain trackers, is because the goal of this project is to bring an un-Googled operating system. Still, many people use and rely on popular apps such as WhatsApp and the option to install them is there for them easily.
What many people do when they don’t want or need apps from the default store, is install something like F-Droid which is an app store exclusively for open-sourced applications.