Fn keys generate ACPI events and not keyboard events. To echo the keypress for Fn to the terminal use ...

sudo acpi_listen

Pres Fn + F12 and it will show

button/volumeup VOLUP 00000080 00000000 K. 

This connects directly to the hardware and is OS independent. Remapping is out of the question.

Here is an interesting read about kernel and a keymap. But that goes beyond a basic changing of keycodes and it does not deal with setting the control key to act as an Fn.