You can always shorten the zippers. You can put a dab of hot glue at the end once you cut it to the appropriate length: a big dab at the bottom of the zipper if you cut that part, or a small dab on either side of the zipper teeth if you shorten it from the top to make "stops" for the zipper head.
If you do still want to do velcro, and you want to go with a back seam, just make sure the boot slip fastens toward the inside; that way, the velcro is relatively hidden from view. If you go with the inside seam, make sure the velcro fastens with the front on top of the rear part.
“Go confidently in the direction of your dreams. Live the life you have imagined.“
- Henry David Thoreau