It definitely makes a difference. If nothing else, always make sure the bleeder valve is above the line input. I had mine backward (passenger on driver side, and vice versa) and could never get a good pedal. Once I figure it out, swapped to the right sides, all was good.
Sorry but you are wrong stating the bleed screw should point straight up. It is tapped into the round bore on a tangent. To bleed from the top it has to point horizontally backward.
I know this from first hand because mine had been swapped by the previous owner and we could not get a good pedal. When I got it the screws pointed straight up like so (view from inside behind driver side):
Looking at the shop manual you can just work out that the screw should point backwards. Once I swapped them it bled really easily.