I think there may be some differences in the inherent definition of the "base". For many, the base seems to be a target in many instances. For example, Create/Mind being the creation of a mind (sentient being, etc). Or Move/Death being the shifting of when you die or somesuch. But even then, that definition is not held in all instances. Protect/Water does not protect water from being harmed, it protects the caster. In the same way, Harm/Fire does not damage fire, it damages a desired target with fire.
While it may cause a slight shifting of mindset in some instances, may I submit that "base" stop being a garbled mixup of target-or-something-else and become akin to the "source" or "form" of the magic. You Harm something WITH Fire. Or you Harm WITH Death. Or your Mind. You Protect in the very same way. Your Protection comes in the form of Water or a Mental barrier. Control and Create become less about Control/Create things that are comprised of the particular "base element/type" and instead are Control/Create USING the particular "base" as a source. Want to convince the horse he should run in your direction but don't have sufficient Mind to Control it that way? Control/Fire could utilize Fire as a rapid-moving, snaking fire-wall to force the horse to go in only the direction you allow it. Create/Water could allow for the creation of a water elemental or perhaps a naiad.
As was mentioned in another thread, Perceive/Fire doesn't need to be knowing how many forest fires are burning in an area- that would be perceiving it as a target. Instead, use it as a source to scry for whatever it is that you want. Perhaps it would still need to have a fire as a source on the other end, but it's still very doable.
Can anyone come up with a combination, looking at "base" as a source instead of a target, that still doesn't seem to work? In my brain, I think all the combinations are entirely viable that way.