MooTools More is a plugins library, it's supposed to use only the external APIs provided by MooTools Core, not any of the internal APIs. An important reason to use the MooTools APIs, rather than the native ones is that consistency is (generally) more important than a little performance gain. Note that, whenever possible, MooTools' own methods will call (and not overwrite) native methods (take your Array.each example, which will call the native Array.forEach where available), and in other cases provide normalisations (take setStyle, and think opacity, for example).
I realise there may be some extreme cases in More that should be optimised (or rather: updated), but in general the above still holds. On top of that, the main reason for the plugins is obviously to have the useful set of plugins, but another reason is to show how to make use of MooTools. Not using Core (or minimally using Core) for More would defeat the purpose of it being a MooTools plugin library, and minimise the learning-MooTools experience when looking through the source. For your own plugins, obviously, you're free to use any MooTools APIs (or none) you prefer. You know best what compatibility you need and when certain optimisations weigh more than the ability to stick to one API.
