If your elements exist as multiple conditions then they will be duplicated. If the same wall exists as different CONDITIONS in the different options than it will be duplicated. There’s no way that I know where you can ConDoc tag more than one LEVEL, ELEMENT, LOCATION, CONDITION to any object. Hence the need for duplication.
ConDoc tags stand alone from SketchUp tags. If using Outliner is working for you then that’s fine. It sounds like your trying to accomplish some things that ConDocs is not suited to doing out of the box. If your goal is to automate the entire process you will definitely need to create some ConDoc tags and modify the appropriate ConDoc scenes in settings to automate. Once you know what option you are developing for CD’s I would save the current model to a new model, strip out the options you aren’t going to use and then tag everything as Level_XX, Element_XX. LOCATION_Exterior, Interior or Site and CONDITION_Demolished, Existing or New. Generate your plans with the ConDoc plan generator and then export to Layot and move on with your CD’s.
I’ve considered modifying ConDoc’s for options as your describing but decided it was easier to have an individual model for each option. Especially sense you’re trying to export them to use in Layout. The rabbit hole can get deep if you allow it and that was the main reason I do this in separate/duplicate models now. When I looked in that rabbit hole I didn’t see the bottom and new it would be a very significant investment that I couldn’t justify knowing I would still have to duplicate things
Hopefully Mike B chimes in. He may have a solution that I’ve yet considered