Anyways, looks like General->Item Manager->Equipment doesn't display items available through your preference options properly, only displaying items currently in your inventory.
Interesting that you conclude that the "proper" functioning of a card which was designed to be "show me equipment in inventory" is to show equipment in storage or closet, as well. There are other tabs to show closet and storage. The tab is actually working exactly as originally intended.
Of course, considering that the "use items from closet" and "use items from storage" options didn't exist when that tab was created, it is unsurprising that it was designed to show only inventory.
I guess you are arguing that any card that is not in the "General" section - i.e., shows just one location container of items - should, effectively, operate on the merged list of available items from all locations that "acquire" will pull from.
That's a reasonable Feature Request. It is to the Item Manager what this one it to the Gear Changer.
Regarding this FR, I will note, at least, that Outfits will pull from closet or storage, as needed, if your settings so dictate. I did that when I was doing PVP and wanted to closet everything important and have KoLmafia pull out outfit pieces when commanded to wear an outfit.