I admit that the help file is extremely misleading when it says "Deleting silence helps maintain video synchronization with audio clips in video editing applications". But after all Delete Silence means what it says, you can't really Mute sections that are already Silent. Perhaps what we need is a method of reducing the level of all audio selected by the detect "Silence" produced Markers.
However there is a different method to produce the effect that you are looking for without altering the length of the audio. That is to using Downward Expansion or Gating in the Amplitude & Compression/ Dynamics processing effect. try the "Noise Gate @ 20dB" preset but move the point between 3 and 2 to around -30dB-->--45dB. You may have to experiment with the settings to match your particular audio.