Hey Steve,
I agree with most of what you've said. However, I would like to point out that while Java might use '$' in the Class.toString() method, the Class.getCanonicalName() uses '.' and using '$' in actual Java code to reference a Class as com.company.Outer$Inner inner = com.company.Outer$Inner.TYPE1 will produce a compilation error. Furthermore IDEs will use the '.' for auto-completion in Strings (like the query specification) when you start typing a FQN. For those reasons I would say that it is definitely unexpected that the query specification would use '$' instead of '.'.