Oh I see what you're asking. You're asking about the alignment of the borders from block to block, not about the colors of the borders.
I always stagger them, like you have in #2. I think if they're all aligned they make the eyes move straight along the aligned seams in the borders and off the quilt, but if they're staggered it keeps the eyes focused inside the quilt and on the blocks inside the boxes.
I like your blocks too, by the way.