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.

nRF Connect is a different world, comes with a lot more options, some really rooted in Zephyr OS, some lessons learned from the prior SDK. And if you're familiar with Linux build configuration system, that is basically what Zephyr brings to the table (comes from Linux foundation). But yeah all that flexibility comes as a penalty when you want simple stuff, compared to ESP32-Sx