These software apps are an expensive over-engineered solution to a very simple problem. First you can not use 'alternate takes' the video editor can only use location audio that belongs to footage in a given scene. In terms of locating room tone or 'fill' this should be recorded seperatley by the location recorder and put in a different folder.
Usually the OMF's we get only contain the audio mixdown from the multitrack recorder on set. Great for video editing, but we need to recapture the 24 bit, 48k audio from set along with all the iso mic channels. We get an EDL from the editor (audio edits only) and then use Titan to re-conform the edit using the higher quality audio.
Then you should tell you video editor to start doing their job, it's thier responsibility to provide you with all available audio edited in place.
I've never heard of anyone working this way.