We won't know until tomorrow night on that - in the Alpha they were NOT in a different folder, just the keys binds file has a version number on it.My guess (from Bruce's OP) is that EDO binds etc are located in a different folder. I could be wrong though
Has they use XML for the configs, unless they completely changed the structure then there wouldn't be a technically reason use a different configuration file for the graphics and sound, the new file format would just have a few new entries that the Horizons client would ignore. The only reason to split to a new folder ( or file version ) would be if the new graphics means people will have to lower setting to play Odyssey vs Horizons. Then splitting the files makes sense.