To my native AmE ear, it sounds a little unusual. Instead, I would expect to hear, "Where are you leaving from?" or "Where are you going there from?" if you know that someone is going from Point A to Point B and you want to know where Point A is.
But I don't know whether the Czech sentence can mean both "coming from" and "going from." If it can mean both, I would consider adding your suggestion. It doesn't feel completely wrong, and it might be used routinely in some geographic areas.
Thank you very much for the detailed explanation. I think it can mean this in Czech. We can also say "Odkud vyrážíš?" (I think it is close to "Where are you leaving from?" and "Odkud přicházíš?" (I think it is close to "Where are you coming from?". But I ask our Czech team for a final decision.
I understand, it has a slightly different logic in English. "Where is this train going?" means "Kam jede tento vlak?", not "Kde jede tento vlak?". I suppose this also applies to people. "Where are you going?" means "Kam jdeš?". Is that so? And "Where are you walking?" - Also? How would you say "Kde se procházíš?" ?
I'd say that "Where are you walking?" would most likely be interpreted as a question about the location in which someone is currently walking. Phone conversation... A: Hi, where are you? -- B: I'm taking a walk. -- A: If you're not too far away, maybe I could join you. Where are you walking? (So, kde here.) If you want to ask a "directional" question about the destination, most likely you would ask, "Where are you walking to?"
On the other hand, "Where is the train going?" would be a "directional" question about the train's destination. (So, kam here.) I think a "locational" question about where the train is currently running is far less likely than one about the location where a person is currently walking, so I won't even go there. :-) I hope this is helpful.