I fully acknowledge this in the article. That is why I sam saying Java and C# will still be around, for precisly the reasons you mention.
My point was that it really just these tools and libraries, and legacy code which keeps these langauges around.
My point was that the whole virtual machine approach underpinning Java and C# has not played out as we expected. People are find with deploying fat binaries or native binaries directly.
Intermediate language just isn't that big of a deal they thought it would be when Java was made. In fact now they all scramble to compile to native code, which kind of proves my point.
The problem is that neither C# nor Java was really designed to be natively compiled and that shows in the limitations of their native compilation solutions.