I put random value between 0 and 50 for that test, but in the final game would be 0-100. At least internally that value can't be changed.
I thought about grouping the item, I even sent an email to Anima about it, however the thing is that you shouldn't really have 500 quantity of one item at any point of the game.
I think I can display the quantity in the inventory itself, like Gold Ore (9).
About the quality, each recipe has a formula, and each ingredient is more or less important based on internal values. For example in one recipe the gold ore could contribute for the 50% to the quality of the end item, while in another could be 75%, or 25% or any other value. That part isn't show because otherwise, the game does everything for you
I need to look again at those Atelier games to see how they do it, since the system is very similar. I don't think they group the ingredients either.
However what you say makes sense, but I'm waiting to see in the final game how much of a problem this is.