Again, do you have an actual study that supports your supposition. A single anecdotal test of one user isn't very convincing.
Let's not take this devil's advocacy thing too far. It's plainly evident that pressing command-s is faster than navigating to File -> Save, given perfect coordination of fingers. What mars any study of this sort of thing is the fact that different people have different levels of coordination, different mental and physical work patterns, etc.
I use a MacBook Pro with a trackpad, and don't use an external mouse, so my right hand is never far from the keyboard. I also keep my left hand on or near the keyboard at all times. And, as I've been touch-typing on a daily basis for probably two and a half decades, I can hit almost any key or key combination I want very quickly, without looking, with a very low error rate. Contrast this with a hunt-and-peck typist who keeps one hand on a mouse, the other hand on top of the desk and the keyboard on a keyboard drawer. If you try to include both of us in a study, the results will be wrong for both of us.
It is my personal belief that anyone who trains himself to use keyboard commands and keeps his off-hand on or near the keyboard will always be faster than someone who only uses one-handed mousing for everything. No, I don't have a study that shows this. It's simply self-evident. Tie one hand behind your back and see how it affects your day... why should doing the same thing with a computer be any different?