I agree that the results in your example are not idea. I’d also appreciate if there was an option to align 8th and 16th rests across the bar (left hand, measure 3, for example). I don’t like it when the rests of a voice don’t line up unless there’s a really good reason due to a particular note’s range.
I agree, especially that manual positioning resets the vertical positioning to zero, whereas what is usually needed is a small nudge. Perhaps there could also be a special setting for a minimum distance between a rest in one voice and a note in another.