Couple of theories. Really as long as it's tillered to match, then it should be fine. It sounds like a lot folks make the bottome limb shorter, probably to clear brush, tree stands, limbs, etc. The opposing (well, not OPPOSING, just different) theory is that the bottom limb should be a tad longer to reduce the stress from being strung repeatedly with the push/pull stringing method that is pretty common with selfbows.
Really though, build it to suit your needs and it should be alright either way.