I don't know what Gary's plans are concerning this, however based on the demo, currently both versions will use the same profile database but different general settings. They can both be installed, but only one should be running at a time, and they're not fully independent.
Though, aside from possible future steam-related features that would require steam version exclusivity, the two versions are essentially the same, and do the same things, so I'm not sure what the utility of owning both would be.