From make menuconfig, I use "Global build settings" -> "Enable IPv6 support in packages" myself. According to the built-in help, this enables / disables the IPv6 support in kernel and packages.
In make kernel_menuconfig there's also "Networking support" -> "Networking options" -> "The IPv6 protocol".
My current understanding is that the first option configures IPv6 support as a "toggle once, configure everywhere" -option; it both enables IPv6 support in the kernel (probably as a loadable module) and causes other package configuration menus to make IPv6-related configs/options available.
The latter option is what actually configures the IPv6 support in the kernel, and can also either cause built-in support or loadable module support. Since the kernel-related configuration files are under source control, I can understand why the IPv6 option is found from the "normal" menuconfig instead: it allows toggling IPv6 on and off without causing changes to files under source control.