kconfig: fix missing choice values in auto.conf

Since commit 00c864f8 ("kconfig: allow all config targets to write
auto.conf if missing"), Kconfig creates include/config/auto.conf in the
defconfig stage when it is missing.

Joonas Kylmälä reported incorrect auto.conf generation under some
circumstances.

To reproduce it, apply the following diff:

|  --- a/arch/arm/configs/imx_v6_v7_defconfig
|  +++ b/arch/arm/configs/imx_v6_v7_defconfig
|  @@ -345,14 +345,7 @@ CONFIG_USB_CONFIGFS_F_MIDI=y
|   CONFIG_USB_CONFIGFS_F_HID=y
|   CONFIG_USB_CONFIGFS_F_UVC=y
|   CONFIG_USB_CONFIGFS_F_PRINTER=y
|  -CONFIG_USB_ZERO=m
|  -CONFIG_USB_AUDIO=m
|  -CONFIG_USB_ETH=m
|  -CONFIG_USB_G_NCM=m
|  -CONFIG_USB_GADGETFS=m
|  -CONFIG_USB_FUNCTIONFS=m
|  -CONFIG_USB_MASS_STORAGE=m
|  -CONFIG_USB_G_SERIAL=m
|  +CONFIG_USB_FUNCTIONFS=y
|   CONFIG_MMC=y
|   CONFIG_MMC_SDHCI=y
|   CONFIG_MMC_SDHCI_PLTFM=y

And then, run:

$ make ARCH=arm mrproper imx_v6_v7_defconfig

You will see CONFIG_USB_FUNCTIONFS=y is correctly contained ...