There is definitely a difference between the two. Might have more to do with the A/D input sensitivity (not available in the FM3), which I dialled up for my low output single coils with the FM9... but whatever is different, I immediately noticed that I had greater headroom in the amp block (dynamic range?) for the same presets that I imported from the FM3. Previously I had to be careful not to max out the amp headroom with too much imput signal from drive or compressors in the FM3 signal chain. Not a problem in the FM9.
I have no idea what's going on under the hood, but I prefer whatever the FM9 is doing