That is not a thing, the variable is named XKB_CONFIG_ROOT, which the extra-layouts module creates by default:
An it should contain a value like /nix/store/01qsglilnjzlczknw9zvh0gmf6h2slcp-xkeyboard-config-2.33/etc/X11/xkb.
~/.config sounds like you are confusing the variable with XDG_CONFIG_HOME (notice the prefix is named after X KeyBoard, not X Desktop Group, and the suffix is root, not home).
I would expect it to work unless there was a regression. Though it probably requires you to re-log in after you rebuild your system since it is not possible to change environment of running programs in general.
As I mentioned, the extra-layouts module already sets the variable, which is then picked up by libxkb & co.