This is true. My theory is that activating the powder measure by hand is typically a little more gentle compared to operating while running (which I find is faster and the action/vibration while loading may allow a little more powder to settle into the bar). Also, when activating by hand, you really need to set aside (recycle) the first few throws as they tend to be a little bit heavier in my experience (if powder has had time to settle more).
I have done that for the same reason, it is easier/faster. But, see my comments above.