> nRF5 is indeed inferior SDK of the 2 (thus abandoned). Also I dislike that a big chunk of the stack there is a binary blob. Regarding the code organization, not sure what toolchain you used, but the latest recommendation for nRF5 (Segger studio) could make it fairly easy to do this, but manually opening the project config files and changing them, not through the GUI.
Yes, I ended up editing the .emProject files by hand. It worked, but it felt like I was doing something wrong. I assume that you are referring to the soft device blob? Has that been abandoned in nRF Connect?