Yes that makes perfect sense, because your are closing the throttle which brings the sync in to play. What I was trying to get at was the sync only has an effect at the closed or slightly open throttle position. This didn't sound like the condition the OP was talking about, but I could be wrong.When you close the throttle at any speed the air bypass is in effect, which is why you can get hesitation when you crack the throttle open and the TB's are out of sync. This can happen at any rpm.
And, the first time I did a TB sync, the engine was noticeably smoother because the TB's were a fair way out.
I'll rely on empirical evidence on this one.
As far as it making a difference at any other throttle position, I will to agree to disagree.