That’s an interesting case. You can try it both ways and see what sounds better. I tried to make them sound listenable when downmixed, since I knew it would be inevitable that it would be heard that way in some cases. My assertion that the stereo mix is preferable for two-channel systems is more of a strong recommendation than an absolute “NO YOU CAN’T DO THAT!” sort of thing. 😉
The main issue when downmixing is that the rear channels contain crosstalk from the front, and are delayed in time compared to the front channels. Inevitably, this results in comb filtering due to not being time-aligned with the front when the channels are recombined into stereo again. I tried to minimize it, but couldn’t eliminate it completely. This will be most noticeable in the first movie, less so in the other two. If you don’t find this to be an issue, then playing the 5.1 on a 3.1 system would certainly still provide a benefit, since you’ll still get the dynamics and extra bass, just not the surroundy-ness. The stereo mix is rather less dynamic and doesn’t have much bass, so on a more powerful sound system it may seem somewhat muted in comparison.
In the next version (assuming again that I have time to do a next version), I’m hoping that this downmixing problem will be much less of an issue.