Never really played Atelier, though I have heard of it before. So really can't comment too much on it. But basic transmutation of metals might be a bit overpowered without the transmutation requiring some difficult to obtain materials. I run a scarcity setting of 10000 on my world gens, which keeps it down to 1 or 2 ore veins on most embarks, scarcity of 100 just seems lame to me. The bright mana gems could be required for some transmutations, and would give them a use beyond making charcoal with. After you get magma, those gems are essentially useless except as decoration.
Not sure what you could do with the addy, personally its killing me right now. As my Koas have stumbled across a large spire of it in the caverns. Haven't started mining it yet, but will probably end up using it for mechanisms.... or maybe some furniture, or decorations. Might dig out a noble room in the spire too, since I can't smelt it into metal obviously. Though a magical reagent in the metal transmutations could work, and you'd be able to get some metal transmuted but it'd be heavily limited by access to raw addy.
Using platinum and aluminum to transmute into your heavy and light-weight ultimate metals respectively would be fine, as both being small clusters only are difficult to come by in great amounts. Most other metals like gold, iron, copper, and silver, if you find them on your embark you will generally have loads of it.