I think, or at least my theory is, that when Shepard became a Spectre, she became independent and was no longer considered Alliance on official records. “Commander” was a title used as a formality, because everyone aboard the Normandy was used to calling her that and it was her proper rank before she was abruptly made a Spectre. Sort of the same way people still call the retired turian general “General” even though he’s… well, no longer a general. You could also factor in her (officially “alleged”) death and her suspicious alliance with a terrorist organization on her return.