Yes, very. The key difference here, I think, is that English emphasises treating the event of missing the train as something that has happened in the past, while Swedish emphasises the state of having missed the train, which is still ongoing. You could very well say "hur kan du ha missat tåget?!" and it wouldn't be odd, albeit a tad less common. For "kunde" to be normal, you would have to discuss a state of having missed the train which is no longer relevant, for instance if you talk about "that time five years ago when I missed the train" or similar. But even then, "hur kunde du?" would feel more natural. We love past tense.
Interesting. Thanks. "How can you have missed the train?" sounds very strange to me in English. For some reason, we feel the need to put both verbs in the past, even when it would seem more logical to say things like "How can you have done that?" (meaning how can you now justify having done that?)