If you apply a dissolve transition in/out on the cue, it should fade out the audio as well when the cue transitions. It currently does not fade in, but we are looking into that. It should fade out though.
The video just needs to be set on end of video to advance, and if it is marked out at a certain point, then it should consider that certain point to be the "end" which it will advance at.
I have attached a video of the end of media setting.