I'm not all that familiar with the Yamahas, Al. Back when I ran them, I had two of the better engine builders of the day build them for me, and I've only refreshed a handful over all my years. I believe they use a cdi ignition, right? I would think that is similar to the pvl used on some Briggs engines today that is programmable. Most people don't realize that the Briggs PVL system has different timing at very low rpm to help start as well, then it's fixed from that point up. The low rpm timing is so low, that I think you don't see it on the dyno because it's generally below the idle rpm.
On the Briggs flathead, the ignition is not digital, it uses the old wound coil. The number of windings, size of wire used, heat, etc affect resistance. They absolutely retard timing as rpm increases. Some do so much more than others. It is very evident with a timing light.