I originally wrote VmX but others have been maintaining and evolving it, so I may be mis-stating things. However ...
For Unavailable and Busy greetings, you should have the choice within the VmX configuration, if you want it to go straight to the recording after your message has been played, or if you want the standard instructions to be played. See the option (on 13): "Voicemail Instructions: Yes/No" If this is not taking affect, this may be a bug.
There was an option introduced to work with temporary greetings as well later on, but it should have been subsequently removed and reverted to the original design, which is, if there's a temporary greeting, VmX is bypassed. (The theory being, a temporary greeting is usually placed as a 'vacation' greeting.) The issue being, there's no way to 'silence' a temporary greeting inside of Voicemail, it's played no matter what as it's designed that way. When it had been added into VmX, it resulted in being played twice and the only solution, outside of modifying Asterisk, was to revert back to the original behavior.