It's hard to take this seriously - do you really call a third-party every-time you rebuild a Dockerfile and run update with your package manager? 99.9% of developers deploying to production do not. If anything the best guard we have is for Debian (as in your example) to realize their keys have been compromised (probably by someone else suffering from such an attack) and alert their users, this has an inherent delay.
> Now compare with any "web crypto": every time the user loads the page he starts back from zero. An attacker can MITM at any time and inject a trivial `form.onsubmit=sendCredentials` and your user is compromised. There is no way to verify out-of-band that the distributed JavaScript is coming from ProtonMail and even if there was, it would have to be done on every page load.
As I wrote above, your concept of verification is quite unrealistic - but even with that I would say it's fair to say the danger of a SSL cert for "web crypto" being compromised is definitely greater than for the desktop since even Dockerfiles are rebuilt far-less than web-pages get reloaded, so a much greater number of users would be affected before they became aware.
I tend to think protonmail is a good thing -- it's obviously not the best choice if you need as many security guarantees as possible, but for general population this is a strong improvement over sell-all-your-data to advertisers google mail.