"Any organization that designs a system (defined broadly) will produce a design whose structure is a copy of the organization's communication structure."

This is a statement about an existing organization and the system they design. It doesn't say you can design a system and then the organization of your choice forms around it.

Bezos had to start with a management edict about how the organization is structured (by threat of firing) to get the SOA system he desired at Amazon. https://plus.google.com/+RipRowan/posts/eVeouesvaVX