I have noticed the same issue in my '04 2.4L 4 spd auto. It seems less pronounced in manual shift, but that may be because I am usually shifting at higher RPM's in manual.
I have also noticed "flare" in auto when accelerating without change gears. Typically in 4th at steady speed on a highway when I give it a little gas, the RPM's will jump a couple 100 and then settle back.
I have just chalked it up to a curious quirk and have not worried about it.
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