I wasn't suggesting conflating Qualities and Items (although in Storynexus there is hardly any distinction between the two) - you are right that the wiki assumes the distinction at too basic a level to change that now. I was merely thinking of having a parent category under that would contain both existing categories and as sub-categories (without changing anything else). But I don't have a good name for it, yet (In Storynexus both things are called "qualities" and what we refer to as qualities on the wiki are called "status qualities"). It's not a major issue but it does occasionally cause awkwardness like the one I described.
I think you are right that a "Quality uses" template might be the right way to go about it.