#1. "RE: Question re: DXO OpticsPro7 and LR4 Workflow" In response to In response to 0
I think you've got the situation pretty well understood. Due to proprietary raw decoding schemes, if you wish to pass images to different editors, it requires rendering a 'baked' RGB image with all the compromises that entails.
Two possible paths are to organize your NEF's more effectively into folders and keep DXO, or try and solve the Lightroom default rendering to get the majority of images closer to what you desire. Are you using Camera-based profiles and ISO-specific defaults?