Doesn't Conway's law make predictions and isn't it falsifiable? You pointed it out yourself "if we look at an org chart for an organization, and we look at the structure of the products that it produces, we would expect them to basically just be collapses of each other [i.e. a homomorphism]"
You could validate these claims by looking at org charts across various companies and looking at their software architecture and come up with some measure for how closely they resemble each other
You could validate these claims by looking at org charts across various companies and looking at their software architecture and come up with some measure for how closely they resemble each other