It's far from obvious. When I read the chapter, I simply assumed that the focus in swords of the Confraternity meant they were really good at producing effects that affected swords. Many would be enchanted in the swords themselves (say, a sword that keeps fighting on its own, or becomes supernaturally sharp). Many would help the confraternity act on existing swords (say, ensuring that no sword ever cuts you, or keeping track where a sword you made is and what use it's being put to). More in general, if you are a swordsmith magus, it seems natural that your Circling Winds of Protection should be Circling Swords of Protection. It never occurred to me until reading it on the forum that if I wanted to make a sword that can cast The Seven League Stride, The Invisible Eye Revealed, and the Incantation of Lightning, such a minor focus would apply -- and as far as I can tell there is nothing in any rulebook saying so (so no need for errata).
I think allowing a focus to apply to enchanting into an item effects that are totally unrelated is a terrible, terrible idea.
First of all, it's incoherent: if a focus in swords applies when you to enchant incantation of lightning in swords, a focus in women should apply when a maga researches and casts the incantation of lightning, and a focus in roses should apply to all magic of a magus whose sigil is roses.
Second (and this applies to the proposed Minor Virtue too): it just runs against the notion of Focus. Your magic is not really Focused, it just faces Deleterious repercussions when you can't use certain vessels for its enchantments.
Finally, it gives even more power to magi focused on enchantment, who have slowly grown in power over the life of the line as bonuses to their work just piled up -- and are not limited by the 10 magnitude cap for non-ritualist casters.