There would be hundreds of names for places, persons or gods recorded in the historical documents. Some of them would be justifiably read in Japanese language, while some are incomprehinsible in Japanese. Some of these become understandable if interpreted in Ainu language which I believe is a decendent language to Jomon language.
I have not arrived at how I could best present examples in an organized way. Before non-doing and only-thinking get too long, I'd start from one example. Pick a choice, from Jinmu-ki, that is, Jinmu chapter of Nihon-Shoki.
In the chapter, there is a description "Iware used to be called either Katawi or Katatachi." If I take a default that one place should have one name for the place, the irregular description tells me that Katawi and Katatachi were of one word, or one meaning. (I have not been able to find an example of two different words representing one same place at one time. It does not mean that such does not exist. However, such would be exceptions, if any found.)
One would easily determine that the first part of the two location names is common, that is, "kata" is common to the two. Indeed, a same kanji is used for both of the "kata". The kanji, incidentally, means "one part of a pair; one (side)".
Then the rest, "wi" and "tachi" are totally different sound. Indeed, different kanji characters are used, meaning "to be (exist)" and "to stand", respectively. It is true that the meaning of the two can be considered similar to each other. However, for a place name, sounds are too different.
In Ainu language, "to be" and "to stand" are said "an" and "as", respectively. (Cf. Selected Ainu Words at [a]. ) That is, sounds for "to be" and "to stand" are similar to each other in Ainu. From its newer (then prevailing) name, Iware, another Ainu word "are" (to sit;to set) is worth mentioning. (are can be construed as a transitive verb of ar.
What could this then mean?
If the very old name for the place was "i-ar-are", invading people could have adopted the sound into Iware and translation of the word as Kata-wi or Kata-tachi. Here, "i" is a prefixing complement (objective) which meaning is "it" or "its". (I feel as if a definite article, "the".) The proposed old name of the place, "i-ar-are", means literally, "its-half-sit". A more meaningful translation could be attempted as "one of the two gods are sitting".
Another interesting episode is around this place. The episode goes like when Jinmu was fighting with Nagasune-hiko in Tomi(nearby location to Iware), lots of hailstones fell down and a shining kite (bird) came. Here, "hailstones" are called "arare" in Japanese.
By the way, "to shine" in Ainu is "tom". Or, shining matter is "tom-i". (Cf. Selected Ainu Words at [t]. ) Remember the name of the battle field, Tomi? And the kite bird is called "tobi" in Japanese.
Visit A person with a tail?.