Lets say for new scene you create a .DazOctane file which will contain all materials in native OTOY definition.
In general, having an additional file which contains scene data can get pretty confusing to users (particularly those less technically inclined). They will move the normal DAZStudio scene file, and not the .DazOctane file and wonder where their materials went. And then renaming the DAZStudio scene file unlinks the 2 files too. All Octane plugins store their data in the host app scene files, and I think this is the way it needs to be.
This way you will have complete control over how the material is stored. I know we will still have some issues with IRAY MDL to OSL / OTOY Native material conversions, but at least after that whatever we do in NGE will be OTOY / OSL material based and will not have any more restrictions.
Moving to a native Octane nodegraph would remove the templating system currently in place, which I think you would agree is essential for supporting the DAZ human figures. The actual storage of the Octane nodegraph is relatively simple, since it is XML and could be stored in the DAZStudio scene file.
I would like to help you write this scene conversion logic for existing scene.
This is something you would need to discuss with OTOY. I think you would need to be able to work full time for a couple of months achieve anything - don't underestimate the magnitude of the task