I haven't tried this but it might work...

Render the song directly to a .wav file (i.e. as the song plays) and the controls like the tempo wheel should be live, so when you want to slow down the song slow down the tempo, for example if you want the last 12 bars to start slowing down, give the tempo wheel a click or two per bar until you reach the end.
Like I said, I haven't tried this but the logic seems workable as long as the controls are still 'live' during recording.