I'm currently redoing some work on the underlying architecture used by the solution.
SDK v1.6 doesn't ship with the native runtime DLLs, which is needed for the PHP Azure extension. You can use SDK v1.6 to package the files, but you still need SDK v1.4 (or at least the files inside bin\runtimes\base\x86) to run the extension.
The steps needed to remote desktop are the same since Azure SDK v1.3, you will have to edit its ServiceDefinition and ServiceConfiguration manually to add this capability.
Unfortunately it's not possible to use Visual Studio with Moodle due to the huge number of files it have.