Off hand, not much difference that I can tell. Pro res is similar to the old lossless hufyuv. DNxHD is more like a low-loss (almost none) x264. The chroma and luma are the factors that affect the green screen quality. Avid is more for Broadcast quality, which blends interlaced fields and blurs them together, which, in turn gives a more “analog” feel to the green screen and motion (it looks like normal Television rather than real life action sharp edges). If you are working in interlaced broadcasts, you won’t go wrong with DNxHD. If you archive and create highlight reels and such, render another in prores, and render an output in prores when you’ve got time.
I keep everything on disc images, which I rat-split and burn to discs for archival. That way I can rebuild any project at any time, and continue working. I use proresLT for most of my non-broadcast work as a full format, and proxy it. I’ve used DNxHD once or twice because it was already in that format when I got the project.
PS
Avid does not prefer DNxHD. DNxHD is a format that was designed to work better with Avid, though AVID will work with almost any installed codec on your system. IF they are on PC and you are on MAC, stick with DNxHD. It is fully compatible and all stages are relatively the same for quality. Pro-res will play back great on both, edit okay on PC, but quality isn’t the best in output.