During Yoruichi's time, the Secret Mobile Corps was NOT a part of the Gotei 13. Its just that in Soi Fong's case, the two posts were merged so that Soi Fong is both a CAPTAIN of the GOTEI 13 as well as COMMANDER IN CHIEF of the Secret Mobile Corps.

Gotei 13 would be more like Marines or Regular Army Corps, while Secret Mobile Corps is perhaps can be likened to Navy SEALS or CIA operatives.

But as of Soi Fon's time, SMC is part of the Gotei 13, making the SMC the Army Rangers rather than as an inteligence agency in their own right.