linux kconfig command line interface

My goal is to change kbuild configs using the command line without messing up dependencies.

For this I've created a 'reference' config by editing my default .config with make menuconfig. The 'only' thing I've changed was changing from 64 bit to 32 bit.

Now I took my original config and applied the following command (from the linux kernel root directory)

scripts/kconfig/merge_config.sh original.conf 32bit.conf

The content of 32bit.conf is simply CONFIG_64=n.

After diffing the two .configs from make menuconfig and my command I see that almost every change from make menuconfig is also present in the other file. But only almost every change.

$ diff .config.mkmenuconfig .config.command104d103< # CONFIG_NO_HZ_FULL is not set112d110< # CONFIG_VIRT_CPU_ACCOUNTING_GEN is not set327d324< # CONFIG_MPSC is not set330d326< # CONFIG_GENERIC_CPU is not set345c341,342< # CONFIG_HPET_TIMER is not set---> CONFIG_HPET_TIMER=y> CONFIG_HPET_EMULATE_RTC=y

Where are these differences from and is there an official way to manipulate kbuild .configs via command line?