I completely agree, I spent the weekend shooting at both, and results were much better shooting at the 3D target.
IMO, it appears that you are shooting better because every arrow after the first, you are actually aiming at your first arrow, rather than a spot on the target. If you really want to know, only shoot one arrow at the 3D target, remove it and note where it hit, them go back and shoot one arrow again, remove it, and continue and see how big your group is. Then do the same on a dot target.
I do the same thing which is why this time of year I only take one arrow out with me and take my time and shoot once at a time. This give me more of a bowhunter mentality rather than a target shooter mentality.
I shoot living things better then any target. I over think targets. when hunting sometimes I think I'm shooting more instinctive than anything.