You can be certain the ECMAScript committee is not going to break any of the more popular libraries (like JQuery, Angular etc) either. It just because these libraries were better designed in the first place that it hasn't been an issue.
https://blog.thoughtram.io/angular/2016/02/01/zones-in-angul...
I can imagine Angular zones becoming problematic in exactly this kind of way in a few years...
While monkey patching in general is problematic, monkey-patching Array or Object is much worse than monkey-patching Window.
In the case of Angular zones, if additional async APIs are added to the browser, Angular needs to be updated to patch them with its own zone implementation.
This wouldn't break existing sites, but could leave, for example, sites on older angular versions unable to use new browser APIs, use libraries that use new browser APIs, or install security updates to dependencies if newer versions rely on new browser APIs.