How to tell apart Japanese and non-Japanese characters in-universe and out-of-universe?
You can't really. It's up to the character designer / artist if they want to give the characters visually distinct race traits, but they're not obligated to and many times they don't, as you noted with Code Geass. The most reliable way to tell if a character is Japanese (without being explicitly told they are) is their name. 

It's best to take things on a case by case basis and use common sense to parse the information the show gives you. If a show is set in Japan, you can safely infer most of the cast will be Japanese regardless of what they look like. If you notice most of the cast look how Japanese people in real life typically look, you can infer that when a blond haired blue eyed character appears, they aren't Japanese. Again, these are assumptions you make based on the context of the show, not universal rules. 

The only universal assumption to make is that visuals in anime are arbitrary and are not obligated to obey any general rules set up for interpreting them.