I was afraid of that. Omni is functional for basic situations, but not very useful when there's any kind of complexity introduced. I don't see a way around your situation without adding another piece of hardware (to filter or redirect the PCs or CCs). You'll drop another $140-160 on adding an 'event processor'.
To be honest, I rarely use XMT. But I do see that option as an all-or-none proposition. Either you transmit MIDI data from the pedal, or the pedal reacts to (and passes through) all MIDI data coming in. Now, you can disable just the PC or the CC transmission [in XMT mode], but that's not going to help you with what's coming in to the pedal from the FCB-1010.
This is a tough one. If a solution comes to me, I'l be sure to reply back. I don't suppose that your amp provides a MIDI Out/Thru jack (admittedly, a long shot here)? Listing the specific amp model might help.