Very Subtle, in Those Examples
You’re right about your examples: a native speaker could answer those questions either way, and the answers would have almost the same meaning. I think people would normally answer in the same tense as the question, but it wouldn’t be unusual to answer “Where did you visit in Japan?” with “I’ve been to Kyoto,” or “Where in japan have you visited?” with “I went to Kyoto.”
However, there are other examples where that isn’t the case (at least in my native American English), and here are some of the ones I thought of. (Or that I have thought of? Either one works.)
Adding a Duration
The present perfect tense is only for durations up to the present.
- “I worked at Spacely Sprockets for ten years,” means that someone has worked there for a total of ten years. That might have been at any time in the past. It might not even have been ten continuous years. I might have left and come back, as long as I accumulated ten years of employment there.
- “I have worked at Spacely Sprockets for ten years,” unambiguously means that I was employed there for the previous ten years, up to the present.
- There’s one weird corner case that I only just realized when I thought about it right now. I cannot say, “*I have worked there ten years ago.” I would need to say, “I worked there ten years ago,” or “I had already worked there by then.” But I could say, “I have worked there, ten years ago.” I think the allowed sentence is not actually present perfect tense, but using the helper verb have for emphasis, so that the actual meaning was, “I indeed worked there, and that was ten years ago.”
At Least Once Ever, That Time, or Repeatedly
The present perfect tense is for things you have done at least once, or have not done even once, ever. The simple past tense is what you use when you talk about a specific occasion in the past, or what you typically or repeatedly used to do.
If you ask me, “Did you visit Kyoto on your trip to Japan?” and I say, “I didn’t go to Kyoto,” I only told you that I did not go there on that occasion. Perhaps I didn’t go to Kyoto then, but I have been there before. If I say, “I haven’t been to Kyoto,” I’m unambiguously saying that I have not ever been to Kyoto, at any time.
If you ask, “Where are you going on your trip to Japan?” and I say, “I have only been to Tokyo, and I would like to see Kyoto,” I’m saying I have been to Tokyo at least once, but maybe more often than that, and to no other location (implicitly, in Japan) in my entire life. The implication is that it’s like there’s a list of places I want to see, and I put a check mark next to Tokyo on that list. If I say, “I went last year and only saw Tokyo, but I’d like to visit Kyoto again,” I have previously been to other places in Japan, but not during the trip that I am talking about.
If you ask, “Did you go to Koganei Park when you lived in Tokyo?” and I say, “I’ve been to Koganei Park,” I’m only telling you that I went there at least once. If I don’t say anything else, the implication’s that I didn’t go back much or at all. If I say, “When I lived in Tokyo, I walked through Koganei Park and enjoyed the cherry trees,” I’m implying it was someplace I went often or habitually, always enjoying the trees. (This implication is even stronger with “I used to go to Koganei Park,” or “I would go to Koganei Park,” and with some verbs, such as “hung out,” more than others, such as “went to.”) It’s possible to override this by giving more detail, though: “I’ve often gone to Koganei Park,” or “I went to Koganei Park once,” clarify that it’s really the opposite. If that’s what you meant, leaving out the quantifiers would sound misleading.