You are so fluent, aren't you? Try to do the same. Look at your first reply in this thread. Is it a kind reply to the poster?
As I said, it is an answer from the market. We avoid the tool that could produce inadequate results. Unfortunately, people do not try to remember such bad experiences, clearly. "I followed the result of tool A, but it was too hard with many stairs." "I followed the result of tool B, but I could not make it. The estimate for the walking time was too short for me." These could be mine or the others with sighs, at that moment. Japanese have faced more occasions to encounter such. At last, those made the trend.
Anyway, HyperDia needs train station names. I use the map to locate them. Then, why not to start from that map. I use GoogleMaps, but there are others. Bing, for example.
Without a JRP, I may suggest to go to Nippori on a Tokyu, then line up a queue at the Tokyo station for a non-reserved seat. Or, take an LCC bus to Tokyo-Yaesu, next to the Shinkansen platform.
For a higher end. I may take a limousine to Tokyo. And take a Nozomi there.
These could be seen on GoogleMaps, but not likely by a train HyperDia. With an advent of GoogleMaps, no experts would be needed. Otherwise, we need to explain in detail why that would be better.
It is the Japan forum only where residents speak of non-GoogleMaps. GoogleMaps is famous in other nation forums in the English speaking community. By the existence of Japan Rail Pass? Then use thishttps://world.jorudan.co.jp/mln/en/japan-rail-pass/
I could not imagine the Japan-Rail-Pass site with a resident HyperDia lover.