Short answer: They're exactly the same. The exact same validation engine is used for both. The FlightCrew project is actually that validation engine, but it also comes with CLI and GUI wrappers to use it.
Long answer: They're not 100% the same, but they are 99.999999999% the same. FC in Sigil doesn't need to perform a few checks (I think a grand total of three) when it's used from Sigil because Sigil removes the need to check if the epub has been assembled properly (since Sigil will assemble it properly when the epub is saved).
But they're the same.
