I was doing some developement for a custom board on NCS v2.9.1 when i noticed some of the changes i was making in my prj.conf weren't being set in the application. My impression was that symbols set in prj.conf have top level priority and overwrite any symbol defaults during merge. I was able to recreate this behavior in the zephyr minimal sample by making the following changes:
In zephyr/samples/basic/minimal/Kconfig:
# Copyright (c) 2023 Synopsys.
#
# SPDX-License-Identifier: Apache-2.0
config SAMPLE_DO_OUTPUT
bool "Do print from the main thread which can be checked"
config PM
default y
config PM_DEVICE
default y
config PM_DEVICE_RUNTIME
default y
source "Kconfig.zephyr"
In zephyr/samples/basic/minimal/prj.conf:
CONFIG_PM=n CONFIG_PM_DEVICE=n CONFIG_PM_DEVICE_RUNTIME=n
When building with: `west build -b nrf5340dk/nrf5340/cpuapp --pristine` I get some Kconfig warnings and the build fails:
warning: PM (defined at /Users/timothy.lee/echo3_ncs/zephyr/samples/basic/minimal/Kconfig:8, soc/silabs/silabs_s2/efr32bg22/Kconfig.defconfig:12, soc/silabs/silabs_s2/efr32bg27/Kconfig.defconfig:12, soc/silabs/silabs_s2/efr32mg24/Kconfig.defconfig:12, soc/renesas/smartbond/da1469x/Kconfig.defconfig:39, subsys/pm/Kconfig:13) was assigned the value 'n' but got the value 'y'. See http://docs.zephyrproject.org/latest/kconfig.html#CONFIG_PM and/or look up PM in the menuconfig/guiconfig interface. The Application Development Primer, Setting Configuration Values, and Kconfig - Tips and Best Practices sections of the manual might be helpful too. warning: PM_DEVICE_RUNTIME (defined at /Users/timothy.lee/echo3_ncs/zephyr/samples/basic/minimal/Kconfig:14, subsys/pm/Kconfig:96) was assigned the value 'n' but got the value 'y'. See http://docs.zephyrproject.org/latest/kconfig.html#CONFIG_PM_DEVICE_RUNTIME and/or look up PM_DEVICE_RUNTIME in the menuconfig/guiconfig interface. The Application Development Primer, Setting Configuration Values, and Kconfig - Tips and Best Practices sections of the manual might be helpful too.
It seems like my prj.conf symbols are being overwritten by the Kconfig defaults. I also found it strange that the buildsys was referencing .defconfigs for silabs SOCs that I wasn't building for. If I turn the defaults in Kconfig to n the build passes as expected.