Many of the aftermarket calipers such as Wilwood have threaded fittings on top and bottom, so you can put the bleeders where you want and plugs in the other holes. Some other thoughts to consider: Access while working on them; suspension movement; fitment of cooling ducts if you should need them later- usually air to the front half of the rotor is easier to do, so the calipers would be to the rear; debris shedding- If the rotor enters the caliper going down, it can trap and hold rocks, dirt, rubber shards, etc on the top of the caliper. If the rotor enters going up, gravity will help fight this problem as some debris will just fall off...
Jay Lutz is a brake engineer. He is right about the brake forces- as long as they are fed back into the axle/spindle/upright, the result is the same.