Sometimes when I work on Thinkpads/MSI laptops, the Ctrl and Fn key are swapped (Fn being the leftmost key), and it drives me nuts - I keep
Sorry. As you mentioned, the Fn key isn't processed by the OS, but received as tuples of Fn + [key] . The best you could probably do would be mapping every Fn + [key] combination to ctrl (and that's only if you never use Fn keys).
Edit: Found this. Before you give up hope, might want to give it a try.