Oh, now you convinced me.

We don't see in any way that he was subordinate to Michael. Michael just treats him that way. He has to stand in line when he wants to talk to him, he gives him orders, etc.
As we know, the Frankie character was a quick fix because Castellano refused to play the original Clemenza character, a subordinate to Vito and perhaps Michael. So we must see Frankie as some kind of variation of Clemenza who inherited the New York empire of the Corleones. Michael let him do his own stuff but he demanded total loyalty and even obedience, even though there was no more hierarchical structure to support that authority.