Spoke with the Captain!
Our arrangement is that the plumbing for the head goes under the wet-locker and then under the aft berth and comes up into the tank at the stern of the boat on the starboard side. If the 'wall' is removed at the aft side of the mattress you can see the tank. This sounds like the long run and big rise you have in your boat too.
Our head works absolutely fine after duplicating the original design. (As a side, my husband also replaced the hose that runs from the head to the tank). He agrees that the design is a bit crazy too, but duplicated it because it worked, allowed us to keep our 30-gallon tank (a very important thing with 4 people onboard), and thought odor would be less. We don't have experience with a flexible tank but he thought it might be more permeable to odor over the long run. He never plans to replace the tank again! My husband's opinion is that you can pump extra water through the system and still be ahead by having double the tank capacity.
If you search for 'holding tank 336' you will find my original post with comments from other users. You could also search about the flexible tanks. I wish we had taken pictures of all this. Our boat is all wrapped up in a tarp for the winter so I can't post any right now.
Hope that helps! I'm sure there are many opinions about the subject.