There are 2 different places for input (keyboard/mouse) stuff. They are separate because the GUI isn't part of the OS and it is just another program.
1 is for the console.
2 is for the display server - i.e. X/Windows or Wayland.
Both need to be modified to work for console and GUI. In X/Windows, there a keyboard map file and some way to deal with specific configurations. I suspect that's what the DEs do ... but if you change to a different DE, then those settings won't come along. I know next to nothing about how Wayland works and suspect it requires the DE settings to control anything, but I don't really know.
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