The reason many deck organizers are set at an angle is so that the lines will run more closely together and lead more fairly into the line clutches. If you mount the deck organizer so that it is parallel to the transom, you'll have the lines about 1.5-2" apart, and if you look at most line clutches, that isn't a good match to how they're spaced.. Also, angling the deck organizers reduces the amount of deck that is covered with lines, since the lines are closer together...reducing the tripping/footing hazard a bit.
I don't see how you can say that setting the deck organizer parallel to the stern changes the contact area... since that is really dependent on the change in angle the line makes when passing through the deck organizer, and any change, given the line clutches and mast being in the same position, is going to be minute—since regardless of the angle the deck organizer is at, the line still has to make a change of about the same amount—assuming the deck organizer is in roughly the same place on the deck.
Using two single line clutches, versus a double line clutch is probably a bad idea as well. IMHO, the double line clutches will be stronger, since they're supported better against all loads. The single line clutch has only two fasteners in line with each other and if you accidentally step on it... you might apply a load in a direction that it can't resist as well as a double line clutch would, since it has four fasteners in a rectangular setup that resists loads in the two directions, rather than just one. Also, the two single line clutches will probably take up more deck space than the double line clutch would...
BTW, having the deck organizers as far aft as possible is a probably a bad idea IMHO... The further aft your deck organizers are, the less likely that they'll lead fair to line clutches and winches, since the deck organizers will be that much closer to the line clutches, and the difference in spacing between the sheaves and the line clutches will be exaggerated by the short distance.
I plan to install a deck organizer too, but not sure how it should be aligned relative to the winch (also replacing clam & regular cleats with rope cluthes...fewer holes and a lot easier to drop a sail in a hurry when single handing). Anyway, it would seem the deck organizer should be installed parallel to the stern rather than at any other angle to minimize the amt. of sheave(?) rolling surface in contact with the halyards and as far aft as possible without having the halyards interfere with anything else topside. I also plan to use two single rope clutches not a double (forward one for the jib, slightly rear one for the main) to avoid possible confusion....labels are fine but seem to wear off quickly). I did see that Lewmar recommends raising the winch enough to achieve a 5 or 10 degree angle on the halyard's entry (to avoid wraps) but in my case the winch is raised anyway by a teak fitting to compensate for the curve in the cabin top.