There is another thread over in General where Rob mentions that this function you are looking for will be in the next emplode. It also could be done in Jemplode too I would think. All that would be required is for the software to send the files to the empeg in the 'correct' track order. I am sure that if you had enough scripting experience, you could even write a little script which would move all the fids around so that they were ordered by track for each source.
But yes, it would make more sense IMO for the player to do this dynamically based on track number rather than fid.