Are we unintentionally designing silos into our organisations?

I was struck when reading this, that perhaps we are unintentionally designing silos into our organisations and experiences because the of method (boxes and arrows / flowcharts) that we are using to map the structures and systems themselves.

Do we need to rethink the use of flowcharts (an engineering-based method) in mapping organisational structures, service ecologies, business models, and particularly customer experiences?