IMPORTANT: The 90 degree discharge fitting on the back of the Superflush rotates 360 degrees, if that helps. I definitely helped me. Loosen the two bolts slightly, rotate the elbow to wherever you want it, and tighten the bolts. You don't need to take the bolts all the way out, just loosen them so the flange has some room. This was not a huge deal for me, but it has helped some. Note that my situation was different from Ted's, because my discharge hose did not come UP from under the previous toilet, through the floor. Instead, it runs behind the toilet after coming through a bulkhead. I rotated the fitting just because it made it a little easier to deal with the process of attaching the hose.
On a similar note, the 90-degree elbow at the back of the bowl could be a much more significant problem up against the hull. This is the fitting that receives flush water FROM the pump going INTO the bowl. On my new toilet, that elbow faces to the right (looking from the front of the bowl). Fortunately, that will work ok, but only because I have enough hose. I would not want to try and re-position the elbow, for fear of over- or under-tightening it. I called Raritan, and they said if it was a problem to go to a hardware store and buy a straight fitting, female NPT(3/4?) to 3/4" hose barb. However, such a fitting may stick out the back of the toilet even further than the current elbow, and then you have to add the room taken up by the "approach" of the hose.
It's not just a straight swap, for sure. The main reason I bought this specific model was to match up with the existing holes for the old Jabsco, and that has ended up being a complete non-factor. The new head will sit on a 2 1/8" riser that I built to sit on top of the "old" floor. I needed that much elevation gain (relative to the curve of the hull liner) for that back-of-the-bowl fitting not to bump the liner.
UPDATE to the middle paragraph: I decided that the elbow fitting at the back of the bowl needed to face strait up to eliminate a hard 180 degree turn for the hose. So I called Raritan again. After I expressed my concern about leaks, and the inability to get to the head of the threaded "bolt" to which the elbow affixes, they told me not to mess with anything but the elbow. Just spin it off, load the male threads up with Teflon tape, and spin the elbow back on. With the correct amount of tape, the fitting tightens perfectly at the right spot.