Your question is confusing because you interchangeably use FM9 and FM3.
The FM9 is running Cygnus, which is the modeling part of Fractal's current generation, as is the FM3. If I remember right, the FM3 got Cygnus after its first update. They sound identical using the same presets and the same modeling version.
Cliff is
always working on new algorithms to improve the sound. He writes for the FX3, gets the code working there, then pushes it to the FM3 and FM9 teams who port it. Currently, we're waiting on the FM9 update, so it's lagging a bit behind the FM3 which has the edge right now, but should be on par with it when it finally drops, and at that point they should generate the same sound given the same preset. So, given the difference between when the teams release their updates, the units should have short windows where there are minor differences, but for the most part they're running the same algorithms and generating the same waveforms because the underlying code is the same.
For instance, I was just updating/syncing some presets between my FM3, FM9 and FX3, and was A/B-ing between the FM3 and FX3 and couldn't tell a difference. That's Fractal's intent.
PS - The
Wiki has a number of pages that compare the units and their capabilities, the progress of modeling, etc. They're worth reading because Cliff is quoted as he discusses this sort of stuff.