Really good discussion in this thread!
I think it's always good to go into anime and manga with the understanding that it's presenting metaphorical truth, not literal truth. The characters are more like symbols than people.
So in the same way as how in a Kabuki theatre performance, you're not meant to literally believe you're watching the story of people with enormous hair and white, black and red face paint who stomp and pose all the time, but a stylised performance, so in manga, you're not meant to believe that people create enormous drops of sweat from their heads when they're anxious, or that they're literally people with blue hair.
Eye and hair shape and colour tend to be stylistic representations of characters in anime. If you see a character with spikey, red hair and wide blue eyes, you can probably assume "this character is energetic and hot-headed, but has a childlike innocence", while a character with smaller, brown or black eyes and dark blue hair slicked down will probably be serious, mature and quiet.
In the same way as a stick figure represents a human, even though it's very distantly abstracted from what a human looks like, manga characters represent archetypes. by exaggerating traits to be larger than life. The bleached, spikey hair associated with delinquency or not fitting into mainstream Japanese society is exaggerated from the sort of red-brown colour it'd be in real life to bright blonde, or sometimes a ditzy character will just be drawn with blonde hair, because she's figuratively "blonde", not literally blonde. Meanwhile a character whose personality or outward persona is the traditional ideal of the "perfect Japanese woman" will nearly always have long, jet black (or blue-black or deep purple, which kind of represent pure raven black) hair (Komi from Komi Can't Communicate, Sailor Mars etc.) because she's representing something more than a literal person.
When a character's defining trait is "white person" they tend to be drawn differently to differentiate them from the metaphorical or stylistically blonde and blue-eyed characters. Usually they're drawn with a larger nose with a higher bridge and a more heavily boned face with strong, sometimes scary cheekbones, and the eyes are often drawn in a more western art style to show that they're from outside Japan and are not a manga archetype. It makes them look intimidating and hard to relate to (because that's the point). But white characters who aren't defined by being white/foreign, tend to be drawn like any other manga character, because in manga, it's the person's archetype or personality that matters most, just like how in Kabuki, the style of face paint or mask and the hairstyle symbolise the person's role in the story.