You need to read the article. It explicitly and IMO satisfactorily answers your excellent questions.

It’s an atrocious system, innocent people get killed every year over it.

So Protonmail was required to log the IP of the user after being ordered to via the proper international Swiss legal channeks, per Swiss/Europol law. And at some point recently, Protonmail thus removed the copy from their frontpage that advertised never tracking IPs.

What the article doesn’t really explain, is what exactly changed about Swiss or euro law? And when? What rules or acts have sprung up that made this possible? Or, was this always something that was possible that has only just now made precedent?

It’s important to hold accountable the named individuals who are harming individual security, safety, and trust in this manner so that they can be prevented from continuing to do so.