1963-66 top question

Hi all,
I have always wondered why some tops when lowered seem to go below the body line while some (like mine) sit like 2 inches above. I wonder if it's a manual vs power top thing? Like that the manual one can be lowered further than the power top (maybe the power cylinders are limiting the travel).
My top aligns nicely with the windshield and looks all good when up, so I don't think it's an adjustment thing. I just always seem to have to stretch the top cover to reach the snaps.
My FSM tells me to lower the top 1/2 way and push OUT the vinyl between the bows so the top folds flatter and doesn't pinch the vinyl. , before I was doing that it sat about 2-3 inches higher and the boot was a monster to get on. After doing it the FSM way I could lower the top into the well and get the boot on easily.