Every case in the article you cited involved someone conducting "research" on computers they did not themselves own, as happens when you portscan a remote host, or look for XSS vulnerabilities on someone's SAAS app, or try to pentest the media system on an airliner.
Project Zero doesn't do any of this kind of research.
Nobody is going to be able to sue Project Zero for finding iOS bugs. You have an almost unlimited right to conduct security research on a phone you buy, or a piece of software you install based on a click-through license.
What you need to be very careful about is, again, testing other people's computing devices. There, you have almost no rights at all (save for services that publicly waive their own rights by standing up bounty programs --- and, don't be confused, Project Zero doesn't depend on Apple's bounty programs to conduct iOS research).
These distinctions are super-clear to people who actually work in this field, but clearly unclear to people outside it, because we end up having the same picky debates about them every time vulnerability research comes up. I get it, it looks fuzzy on the outside. But it is not fuzzy to practitioners; the rules you have to be aware of to conduct research are actually fairly straightforward. Don't mess with other people's machines.