It is actually a 1950's fishing restriction law. There used to be a lot of float fisherman on the Lewis river (between the lakes) and they were getting pretty overfished so they made a no fishing from boats rule on the Lewis River, which they have made into a ban on floating at all on the rivers in the park. Even though you can run a motorboat all day on the lake.
The AW proposal(probably online somewhere, ask Gangemi) is widely acknowledged to have asked for far too much. For example they asked to be able to float the Lamar Valley, which is packed shoulder to shoulder with people watching wildlife, it is one of the most wildlife packed areas in the park and AW asked to be able to float down through the thousands of buffalo and elk and wolves. However maybe they were figuring they could give up a couple to get a couple.
In the Park Services written response to AW(probably available online, I have a hard copy that was part of our 120 page indictment) to why they do not allow boating in the Grand Canyon the Black Canyon section was that Peregrine Falcons nested there and would be disturbed by boaters. This seems strange since there are fisherman everywhere and I have yet to see a Peregrine Falcon be "scared" of me. In fact I watched one hunt Pelicans for an hour on Beartrap Canyon once and it did'nt even notice me.