I'd run with the same gain on both channels. Probably not a huge deal, but if you are coming close to 0 on both channels and then add them together in post, you may end up with clipping or having to reduce the gain before you decode anyway. Also, if you boost the gain on the side, you will need to put much less side in the final mix to get the right image than if you'd run both channels at the same gain.
I'd say M/S has the potential for less chatter, if you go with a mid heavy mix.