I think there's a useful distinction to be made between "we understand it" and "we can make use of it." Certainly the latter is true, as you describe in your examples. I don't know that it implies the former, though.
I mean heck, even something as mundane as concrete is still the subject of active research as to the chemical reactions and complexities involved.
I guess it's more a spectrum of understanding than a yes/no situation.
For myself, I find it exciting to keep discovering how little we understand, despite our abilities. We seem to be barely a step removed from alchemy, from some points of view.