I don't see why this is a problem. As long as you don't change the interface of Bar, it makes no difference how you implement that interface. None of the client code using Bar knows anything about System::Bar, etc.

The suggestion of using a factory addresses this because the factory deals with System::Bar - a namespace that can stay unique - while providing objects that can have their namespace location be moot. That is, the factory provides an object with the Bar interface but whether it's implemented as Custom::Bar or System::Bar is irrelevant.

There's no reason that the Bar class has to implement anything at all. Calling Bar->new() could just return an instance of Custom::Bar, or Bar could simply inherit all of its methods from Custom::Bar. It's the same thing as using a factory. The only difference is that with the factory you change the name of the class to use by modifying the factory class or its configuration, while without a factory you modify the Bar class to tell it what class to return.