(They want to do that because alert() "stops the world" by blocking the main thread event loop, and because they make it easy for a site to post a message that appears to come from Chrome itself, or from another website.)
https://groups.google.com/a/chromium.org/g/blink-dev/c/hTOXi...
> We’re on a long, slow path to deprecate and remove window.alert/confirm/prompt and beforeunload handlers due to their role in user-hostile event loop pausing, as well as phishing and other abuse mechanisms. We’ve been successfully chipping away at them in various cases, e.g. background tabs, subframes with no user interaction, and now cross-origin subframes. Each step is hard-fought progress toward the eventual goal, and we should consider carefully whether we want to regress, even in an opt-in manner.
Rich Harris has a good blog post about this. https://dev.to/richharris/stay-alert-d