This is the crux of the piece:

The data is said to have been used to attempt to tie anonymous users of messaging apps to specific Apple or Google accounts.
...
metadata (like which apps are sending notifications and how often) is not encrypted, potentially giving anyone with access to the information insight into users' app usage.

I wonder what the devs for apps like Signal and Telegram think about this. Afterall, their stand the most to lose is nation-states figure out how to track users using push notifications. The lives of their users could be at stake.