- an office building for whatever is located 1 mile away from whatever else... by that standard any NGO based in Paris or Washington cooperates with intelligence services ;)
- some shares of this private company are owned by reputable bad actors... by that standard any private corporation is malicious ;)
But yes they did behave like a honeypot ("all your data is safe and anonymous with us") all the while using "custom" (well openpgp.js i believe?) encryption strategies relying on good-faith servers. Moreover, i found it weird that a research project would have such marketing power... it's famous in IT circles that uni projects have great code but the worst PR :) (ever heard of GNU/Net? :D)
Overall, i think you may be imagining things and a title claiming "TRUTH" about proton doesn't help your case because you have little evidence. However, i believe no matter the conclusions you draw from them, the correlations you present in that article are of public interest because we may learn in the future that there were indeed hidden connections to intelligence services (of which you don't yet provide proof).
If i were you, i would certainly rename the article to "Disturbing facts" or "Alleged truth" but not claim it's an absolute truth, because you don't have hard evidence. And i would certainly add two new bullet points about:
1) Protonmail collaborating with EUROPOL in a clear case of political repression against anti-gentrification activists in Paris (and apparently they are the ones who suggested french police requested via EUROPOL), and setup IP logging specifically for that user... so even in the clearest violations they are not standing up for users if it means taking legal risks for them
2) Prontonmail joining the long list of censor trolls asking registrars about identity of domain owner?! (see also previous threads about Njalla and Peter Sunde disappointed in Proton) They broke away from a tradition of free speech (debunk claims publicly), and from a traditional form of law enforcement (first contact website owner, if it fails contact the host if the contact is obviously illegal , or just sue against X for defamation)
Time for some Streisand Effect?
 Yes contacting the registrar to obtain information or censor information is rather unusual. And let's be honest, beyond usual corporate trolls with armies of lawyers, contacting anyone to censor such vague claims on a random blog in a dark corner of the internet is also rather unusual. It's not exactly like the website is reachable at protonmailtruth.ch or whatever.