i don't think it's about visual design. Having a signalling mechanism that lives outside of the dom is confusing to users, and alert is a rare exception from wayyyy back when. It looks like google is doing this for user security, and I support it.
I don't support the way they're going about it. If Mozilla and Microsoft and W3C are willing to get on board, I would greatly support it. But this is more throwing their weight around, and it sucks!
>existing web
i'm gonna be honest, i havent seen a meaningful alert be used in recent memory, and i work with a lot of web apps. All alert()s could be easily replaced with something inline. I'm not a huge fan of breaking changes, but this is one (with a multi year rollout) that I would support.
I see them used very often to indicate unsaved changes when a user leaves a page.
Calls to alert(), confirm() and prompt() cannot be polyfilled or safely replaced in the general case because they explicitly block the main thread. That behaviour might not be desirable, but it was the path chosen when the relevant code was written. While some maintained applications will be able to switch to asynchronous alternatives, many older and unmaintained websites - the long tail of the web, will stop working.
Now if you wander down the wrong internet 'alley' you'll get mugged by someone using alert() to almost completely hijack your normal session. Especially for older folks (my grandpa really suffered from this), it becomes impossible - to the point they'll even call someone up and give them their credit card number sometimes so they can 'get to their email'.
Warnings to the dev console won't stop this type of harassment of users - only stopping it from being the modal dialog it is supposed to be (per alert() prior behavior) will.
"Protecting the users" is an absolute lie.