IMHO, Scrum is a tool bring an agile development process to a classical project organization. The idea behind Scrum is to build your own 'bubble' (the development team) where you can use an agile approach while assigning people who are meant to manage the interactions with the rest of the organization (Scrum Masters).
So in the end, Scrum is some kind of practical approach to bringing agile development practices to large organizations and obviously, that is a compromise. So there is no contradiction, it is just that Scrum is not the solution, but a (first stage) tool to change existing organizations to become the agile organizations we would like to work within.
Sadly many companies think they are 'Agile' once they adopted Scrum, but often they embraced the 'Processes and Tools' while agile clearly states that 'Individuals and interactions' are the relevant part: