You may place any minor items from your hand under Armory during your organization phase.
You seem to have forgotten that storing is only one of the ways of putting an item under Armory.
Also, certain cards *do* place other cards off to the side. Armory is not one of these cards. Cards that place things off to the side are:
1) Prisoner cards, by rule (Dark Minions insert, Taking Prisoners); and
2) Those with explicit text to that effect (Sacrifice of Form, Rumours of Rings, various hazards, etc.)
At the risk of being pedantic, the indications are that your reading of Armory is flawed.
The idea that Armory only changes the source of the item follows neither from the card text (where one plays an item under Armory *instead* of following a normal process) nor from any rule you have cited, and, indeed, you have just cited rules that have little or even nothing to do with Armory's text.
(Note also that the item is stored to Armory *instead* of to your MP pile -- the normal process and rules do not apply. Otherwise, by rule, items stored under Armory can never be played -- MELE p. 48, Storing Cards.)
The game is flawed, but this does not mean it cannot be loved.