C# in the .Net 1.0 era was very similar to Java. However, most of the domain-specific knowledge is not in the language, but in the associated class library and runtime. Usage patterns evolve with them.
So, under the assumption that Scala.Net will get traction, in three years, people will be hiring Scala.Net and Scala(JVM) programmers. Educational programs will teaching two different flavors. Books will describe two different flavors.
How does this help Scala or the Scala programmer?
(Then there are more questions, such as: what does Scala.Net offer over C# (which is incorporating functional constructs) and F#?)