Everyone should be using MooTools now. The ECMAScript committee has basically made it an unofficial extension of the language by vowing never to break that library. Guaranteeing its stability for years to come.
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.