In Arizona, Humphreys Peak simply refers to the highpoint along the west ridge/crater. The name of the whole mountain mass is more properly referred to as the San Francisco Peaks. From Flagstaff, Humphreys isn't even visible: the big foreground peak is Mt. Agassiz. But by convention the whole mountain is often referred to as Humphreys Peak, without loss of confusion.
Most peaks' names were given by the early explorers or surveyors and stuck because either the peak didn't have a name originally, or had some unpronouncable local name (e.g. The Navajo name for the San Francisco Peaks is something quite bizarre. I don't have it handy now but can look it up at the ASU map library, where I'm headed to soon anyway). So most peak names simply stuck by default.
California: Mt. Whitney isn't obvious from below. Inyo Peak looks bigger from below. Did the early native peoples have a name for the bump that is now Mt. Whitney?
Nevada: Boundary is pretty bland, but I guess it's appropriate. Maybe we can propogate the story of the famous 1850s surveyor Ebenezer Boundary. who made the crucial discovery of straight lines on the ground that delineate and separate various political divisions, thus making the peak's name very appropriate.