It's the way they decided to implement it. I told the product manager that it's a very, very bad solution, as it means using an FS-100 in the field means you can't let the audio guy hear playback for sound, etc. I hope that they address it whenever they do another firmware update.
I think the following link might prove to be helpful for questions on the FS100 and frame rates (I still receive many calls about compatability, and with the Cineporter now being phantomware, this will likely come under heavier spotlight:
Regarding audio playback, I found this post off-site:
"Actually, audio is NOT always muted on the FS-100/HVX200 combo. If I shoot in NON-NATIVE modes (no PN), the audio plays back fine. I do this regularly with clients on ver3.0 drives. I just tested again and did both P2 and Quicktime files (non PN) and played them back in the camera with clear audio."