Until I read this I didn't know about the global foot expression pedal assignment! I thought I was stuck manually assigning it to every patch.
No matter how awesome it is though, I don't think I can really use it since it isn't overridable per-patch unfortunately.
Like the OP says, it seems if you assign it globally to LPF then the mod matrix will ignore it completely. I wish I could say "half LPF" globally, but then also use the foot control to mod the noise amount or oscillator mix.