This checks generated config after Kconfig pass if it still contains preferences we have in files in configs directory.
This also drops some of the options in our config that are obsolete or invalid.
CONFIG_VERSION_REPO is overwritten by setting pushed dynamically in config by compile_pkgs so it makes no sense to have it here.
CONFIG_BUSYBOX_DEFAULT_CROND seems to be impossible to change and is also default value that we later override with CONFIG_BUSYBOX_CONFIG_CROND.
All PACKAGE options are not necessary. They are all enabled to 'm' but getting them to 'y' would require a lot of works with gain that build would in some cases failed instead of passed without that package. Not worth it.
CONFIG_DEFAULT_TARGET_OPTIMIZATION is not applies so it is dropped here without replacement. Same as one occurrence of CONFIG_CPU_TYPE.
On notice to @jschlehofer because of configuration change.