It's important to differentiate between using a network as a template when you create your networks (by copying settings) and BINDING a network to a template.
If you bind a network to a template, a bunch of things can only be changed in the template. Those changes get applied to all of the bound networks.
I'm in the middle of testing some changes that will roll out to a few hundred locations. I copied the template and made the changes in the new template. While visiting a test location, I re-bound the network to the new template and waited a couple of minutes. I was then able to test the changes. This also allows easy rollback. When I'm ready to move the rest of the networks, it's a simple matter of 'select all' and rebind.
If you use the Scanning API, watch out. When you copy a template, the post URLs don't get copied over. That's the only thing I've found that fails to copy over. There might be others.
For your situation, there is Organization > Configuration Sync to view differences between networks. I've never been able to get useful results, but I didn't try very hard. YMMV