We don't see in any way that he was subordinate to Michael. Michael just treats him that way.
Are you sure you've seen the movie, because taken aside a drunk Frankie at Anthony's communion celebration, he acts subordinate to Michael in about every way. Michael ordered Frankie to make peace with the Rosatos, because he was
doing important business with Hyman Roth and didn't want it disturbed, and Frankie followed those orders, even though he hated the Rosatos and wanted to eliminate them.
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.
There was still an official hierarchy, confirmed by the chart that was shown at the Senate hearings. Those are the
facts presented by the film. As to whether the chart was accurate or not is mere speculation and depends on your own imagination, also known as
fanfiction.
