Because I am 70% sure it is doing something that it isn't supposed to do and it is a bug. You can choose to call it an 'undocumented feature' if you wish. This is rather similar to the Risia bug where you could get both frost and icy burst on an item, which they did fix. Obviously they don't feel the double random focus is as big of a deal since it has been occurring since at least 2007, but that doesn't mean it is not a bug.
And I already said I agree that spell penetration should be available as both a prefix and a suffix for crafting, since it is available to the randomizer as such. To further clarify my point-of-view, yes I do think that each and every prefix and suffix that is available to the randomizer should be available for crafting, and the ML should also end up being the same as it would if it was from the randomizer. Maybe even one or two lower for bound stuff.
But crafting is not even fully released yet and we can't say if some of the things currently missing are simply part of the higher level stuff and we simply need some broccoli to craft it.