Don't know if --old-config et cetera do or not. I suspect not. Those options should affect what happens to the config
after it has been selected.
I would not keep even backups in /usr/src/linux. Genkernel and the kernel make process do too much there.
This is what I do:
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zcat /proc/config.gz >/root/config.now && genkernel --menuconfig --install --kernel-config=/root/config.now --bootloader=grub all
That depends on having CONFIG_IKCONFIG and CONFIG_IKCONFIG_PROC set. Currently, they are under "general setup" ->"kernel .config support" and "general setup"->" Enable access to .config through /proc/config.gz" in the menu. This feature is handu for checking your running kernel.
Which version of genkernel are you running? Mine is 3.4.52.2
Genkernel is written in bash. If you read shell, you can figure out what it does. I did that to figure out how it was updating /boot/grub/grub.conf so I could steal the code. It wasn't easy to figure out, but then I'm very weak at shell.