Hang on,
So you have the correct keyboard layout at a console login now, but not in Kodi ?
Did you go into Kodi’s International settings and choose your language and keyboard layout there ?
Settings->Appearance->International, you have Language, Region, Character Set, Keyboard layouts and Timezone country and timezone all available.
Timezone is shared between Kodi and local console but the other settings are independent between console and Kodi.
BTW we leave the keyboard-configuration package out by default because it interferes with the splash screen and slows boot quite significantly for something that 90% of users will never use. (Local console login with a non US keyboard layout - you don’t need keyboard-configuration for Kodi keyboard layouts)
Unfortunately there is no easy way for us to include just the keyboard layout parts of keyboard-configuration without it trying to set console fonts (thus wiping the splash screen) and adding various startup services that we don’t want or need, hence leaving it out by default.