OPENTHREAD_MANUAL_START was assigned the value 'n' but got the value 'y'

I am building a Thread Coprocess using the nRF Thread Coprocessor template. Everything seems to work fine except when I use the OPENTHREAD_MANUAL_START=n config in the prj.conf file. The build process ignores the relevant flag and shows the following warning:

warning: OPENTHREAD_MANUAL_START (defined at
/opt/nordic/ncs/v2.2.0/nrf/subsys/net/openthread/Kconfig.defconfig:77,
subsys/net/l2/openthread/Kconfig:49) was assigned the value 'n' but got the value 'y'. See
http://docs.zephyrproject.org/latest/kconfig.html#CONFIG_OPENTHREAD_MANUAL_START and/or look up
OPENTHREAD_MANUAL_START 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.

I even manually edited the Kconfig configuration from the /build/zephyr/.config, but that still reset to the default configuration during the build process.
However, when I comment out the following two flags from prj.conf, that resolves this, but I cannot comment out those two flags since these are essential for the project.

CONFIG_OPENTHREAD_COPROCESSOR=y
CONFIG_OPENTHREAD_COPROCESSOR_RCP=y

Does anyone know how I can make the OPENTHREAD_MANUAL_START=n work?

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