One of the authors here. Deis is better at the moment, supporting clusters, as well as being coreOS based (which is one of our goals as well). Back in october/november, when the project was started, we were ahead for some time, but I ran out of time to work on it. So recently, I found more time and ended up open-sourcing it, hoping to get more contributors onboard.
Yes, we technically could collaborate with Deis, though they a different programming language (python). I also have a few concerns doing major contributions, since Deis developers' company basically makes money off of Deis via consulting -- I'd probably prefer to join the Flynn camp (https://flynn.io/).