Trying to figure out such a scenario myself. I think I will not use the branching approach but a customer build using msbuild. You run msbuild with /p:customer=customer1
and have in your project file an
<ItemGroup Include='%(customer).config'>
<Link>app.config</Link>
</ItemGroup>
Then in your app you have a app.config file included that contains the content of each customers config.
If you have a new customer you just add another newcustomer.config
file and build the app with msbuild projecfile /p:customer=newcustomer
or have a clever batch msbuild that finds all *.config files and builds the projects for them.