I couldn't be sure from the photo, but Bonneteau's cranks did look unnaturally short. Just look at the height of his right knee at maximum flexion; the knee cap is only slightly higher than his head! When you think about it, that small amount of knee bend must give him a big aero advantage.
I ran an experiment on my upright today that bears out what you report about hip angle. I had always suspected that I made more power on the uprights when I sat up with my hands on the hoods rather than down in the drops, so today I went up my favorite test hill where I always try to hold the highest average power I can manage until I reach the top. My previous record was ~460 watts on the upright with my hands in the drops, and ~395 watts on the M5. Today I managed to average 516 watts with my hands on the hoods, and it would have been even higher had I not miscalculated the starting point of the segment. A 56 watt difference is huge, and I can really tell the difference when I change my hand position from the hoods to the drops; it suddenly feels as if my quadriceps have no leverage, and my glutes are being asked to take up the slack, which they're just not capable of doing.
In anticipation of buying a new aero helmet, I also did a short but steady run at 27 mph. Now I have the data I need to tell me how much the choice of helmet really matters. Next, I'll do the same segment at the same speed wearing my LG time trial helmet and see what kind of wattage reduction I get. If I'm going to shell out 400-500 bucks on a new helmet, I want to make certain it's money well spent.
Larry posted his write-up on the "Frankenbike" on a racing forum I've since been banned from, so I can't go back and look it up. What I remember him saying was that it was indeed much faster at the same power level than the V20 out of the gate, but that only lasted for a short while until his heart rate began to climb much higher than he was used to and the effort became impossible to sustain. I think he gave up riding it after that and focused all his efforts on the Arrowhead. Larry sent me some spreadsheets where he'd recorded his results on various recumbents, testing different wheels and tires, etc., but the Frankenbike isn't mentioned anywhere. That suggests to me that his performance on it was so poor that he'd simply written it off after the first experience. Nevertheless, I'd love to get a test ride on a radical design like Bonneteau's M5, if only to satisfy my own curiosity.