Yes, you're absolutely right WB imports split stereo in such a weird manner. I never had to work with this format in WB, so I had to test it before I could comment. I also found out that if you pick the L part only, of the split audio file, and drag it into WB then both (L&R), do get imported. So you don't have to worry about that I guess. The naming convention seems strange, but it is meant to operate that way I think, only showing one audio file. You can easily rename it under CD Tracks. What is disturbing though is that in the overview window one only sees the Left side of the audio, underneath it however both sides show up correctly.
All in all WB still works, which is surprising considering that it is not supported by apple anymore!