I'm developing a script controller for Ableton LIVE to support the Atom pad. After a bit of reverse engineering seems to me that in MIDI mode inputs are disabled and you can not turn on pad lights. In order to use the native mode in any other DAW you just need to send the secret hand shake, which is a C-2 note off 127 velocity to the channel 16 (midi tuple (143,0,127)) to the ATOM pad. I still do not have a complete MIDI output chart and I'm working on it, in order to see the MIDI output messages just use a MIDI sniffer such as MIDI monitor.
Always free the hardware from software slavery.