PassKeeper | Windows utility that allows you to keep an encrypted list | Encryption library

[You are asking two questions. I will answer only the question about saving the linux .config file; the other question is too generic.]

You need to set the appropriate options in menuconfig, not just override on the command line, otherwise they are inconsistent.

The process complete for creating a linux defconfig based on a pre-existing in-tree defconfig is the following. You have already done steps 1, 2 and 3.

1. In the Buildroot configuration, select BR2_LINUX_KERNEL_USE_DEFCONFIG or BR2_LINUX_KERNEL_USE_ARCH_DEFAULT_CONFIG.
2. Run make linux-menuconfig and adapt the linux configuration to your needs.
3. Build and test, iterate over 2 until you have the configuration you want.
4. In the Buildroot configuration, switch to BR2_LINUX_KERNEL_USE_CUSTOM_CONFIG and set BR2_LINUX_KERNEL_CUSTOM_CONFIG_FILE to the place where you want to save it (typically board/passkeeper/linux.config or $(BR2_EXTERNAL_PASSKEEPER)/board/passkeeper/linux.config if you are using an external).
5. Run make linux-update-defconfig. It is essential you do this before doing anything else, otherwise Buildroot will complain that the file doesn't exist.