In a configuration without the OEM CATs, the FRPP retains the O2 catalyst check (hence the CA EO certification) and will most certainly trigger a CEL. If you don't want a CEL, you'll need a tuner such as Torrie to turn off the O2 test. You can still pass CA visual like this as well as the OBD2 hook-up because (currently) CA still allows for one monitor incomplete status. However, no chance in hell that a Ford GT can pass the CA emissions sniff test without the CATs.
When I ordered the FRPP tune, I advised the tech that I was using the FRPP headers and muffler and I was specifically concerned about a CEL. I was told the tune was compatible. in any event, I never had a CEL when I ran the tune. Perhaps the catalyst check was modified in the tune?