I have that problem too, on my road bike set up with TT bars when I'm on the bars, and I also ride a 47cm frame. I'm kneeing myself in the ribs, though, not the gut, so it's not a weight-loss issue. My friend suggested that with a very low aero position, I may need shorter cranks to compensate.

I'm wondering if there's just a short-person geometry component here, like the way little bikes have toe-overlap, little bikes might just be prone to this issue. Shorter cranks, shallower drops, a more forward and higher saddle position are the things I would try. If you're not racing, the shallower drops makes the most sense.