Bug was this sequence:
1. old sdkconfig file has some settings (maybe target=esp32s2beta)
2. idf.py builds a new sdkconfig.defaults file with full new settings
3. new settings includes something that conflicts with the old settings (for example,
CONFIG_IDF_TARGET=esp32 and BT_ENABLE=y)
4. confgen tries to apply the new "defaults" to the existing sdkconfig, settings end up a mix of both due to the conflicts
Fix is to generate the sdkconfig file directly.