Object or Function prototype mutability is unintuitive, like a key that returns a different letter on each keypress. This points to one of the reasons why patterns like virtualization via proxies and reflection, functional programming's eschewal of side effects, and reactive vue-style object mutation events are commonly used, especially in conjunction with composition techniques.
That is, we expect Function.prototype.apply to invoke a function given context and an array of parameters. We can easily change the method - Function.prototype.apply = ( fn ) => { console.log( fn ) } - it is expectations that are difficult to change.