With two exceptions common to most magi (Locate Object, Identify), every spell in the Transmuter repertoire is currently in your second category. More specifically, I'd give the domain of Transmutation as 'temporary manipulation of living matter'. Permanence, dead/inanimate matter, creation, and destruction eluide the transmuter.

The other categories you discuss have to do with other schools of magic that are established in several IC sources. The problem with combining them is that you lose the class's unique identity- they either share a bunch of spells, or we might as well do them as a separate class. While I don't like the idea of blending them, it's conceivable that abilities from those categories will enter PC hands at some point in the future.

valguarnera@carrionfields.com