Iirc, the reason you end up hitting the limit for 65k methods is that each library tends to keep independent copies of its dependencies. This simplifies dependency control, but ends up mushrooming quickly.
The code for the binding classes lives in retrofit.adapter.{guava|rxjava|…} [0] but the respective library still lives in its usual package. [1]
If that weren't the case you could A) not manually provide a minor version via your dependencies block in your build script and B) would have interop problems between libraries and between a library and your code as the same interface copied to a different packages is not the same interface for Java.
[0] https://github.com/square/retrofit/tree/master/retrofit-adap...
[1] https://github.com/square/retrofit/blob/master/retrofit-adap...