Not having the lines line up has no effect at all, or it has lots of effect, just as you wanted. It really depends on what car you are chopping and your plans of how to accomplish the task.
On the body you see the "B" pillar (middle post) is probably being cut up higher so the cut will miss the upper door hinge. On the front post ("A" pillar) it is probably down lower because the post is the same diameter around at that area but tapers down smaller or something up higher.
On some cars you may even want the cut to be at an angle from one window to the next. It all depends on where the parts are going to line up WHERE you cut it.
A top doesn't come STRAIGHT down when you remove a portion of the posts. On some cars, yes. A Ford Model A for instance, the top comes STRAIGHT down (all models but the 31 Vicky) Cut 3 inches out of the posts and drop it, it doesn't matter much where you do it, just cut the roof off, cut 3 inches off the post and drop it back down, and you everything will line up. The windshield posts do have a taper WITHIN them that you have to take care of but the post in relation to the others is perfectly vertical. So the back side of the windshield post at least is perfectly vertical.
On the Model A it is like shortening a cardboard box. Just cut a strip out and the box is smaller.
On other cars, it is more like cutting a strip out of a ice cream cone. When you remove the strip the top piece won't fit onto the bottom piece. Almost every single body has this effect to some degree, some worse than others. So even a super simple body like a truck cab where you know there is a slight windshield rearword post lean, there is also a lean on rear cab as well as the front leaning IN from the sides. Sometimes a cut on one post five inches up from the bottom would allow the roof to come right down and mate with it's new location. While that same car may need another post cut eight inches up from the bottom for THAT post to line up.
Hope that explains it for you.