I worked as a programmer at several IT firms which practiced Agile in some form or other, there used to be stand-ups, scrums, TDD, code reviews and even peer coding but not once did I find anyone have issues with following hierarchy or seniority of order in teams. That's not to say that hierarchies are a pristine thing, they have their share of problems too.

Even many Project Managers aren't an ideal to follow, there are those who try to screw the happiness out of every team member, there are also those who are experts at shrugging responsibility and pass on the blame to others. But on the other hand, I've met some great ones too who are an inspiration to their teams, who everyone in their team respects a lot and like to vouch for.

