A person's job prospects may also be limited if they don't know, or are not comfortable with, what the majority uses
At that age, what matters isn't any of the material learned. It's the attitudes and self-conceptions that matter. If a five-year-old learns that he likes telling computers what to do and that he can get steadily better at it by exploring, that's a huge win for his future.
If you can learn how to run first, it should be pretty darn easy to learn how to walk afterwards.
Last winter, I suddenly had to fix problems in Windows Server 2008. I may have been a bit slow, but yes, I can fix an OS I've never used.
If you have a good knowledge base, and the experience to provide a good intuition, you can figure them out.
I would, incidentally, consider Debian to be a modern OS, and a CLI to be a modern UI. If they can string together commands in bash, I'm sure they'll be just fine with Windows.