I also found an interesting mention to another rare traditional Japanese variety, named Hanaharu. ( 花良治みかん )
"The biggest feature is the unique refined fragrance not found in other citrus fruits. The scent is very strong, and when you begin to peel it, a good scent spreads throughout the area. There are basically no seeds, an exquisite balance of sweet and sour taste, a delicious taste even when it is blue, and an exceptional quality that is unparalleled.
A study by Kagoshima University that Hanaharu oranges may have originated from Kunenbo as a seed parent and Kikai oranges as a pollen parent"
https://www.kerajiya.com/shopdetail/018000000001/I found another reference here that there is a production area for Keraji in Higashiizu. (Looking on a map, this appears to be considerably farther north, only a little south from Tokyo)
The article alluded to the fact that this variety was very hard to find.
"The other day, I participated in the Marche held in the basement of Yukiyuki Street in front of Tokyo Station. During this period, various citrus fruits are lined up in the Marche, from light lemon-colored Fudan to red blood orange. Every time the shop peels off the preparations for the tasting, a refreshing fragrance spreads and heals the fatigue of work.
There was an unusual thing to see for the first time among such citrus fruits.
Its name is “Keraji”. It seems to be a phantom, and the production area is Higashiizu. Originally it is native to the Keraji district of Kikaijima. Thank you for taking one of the tasting "I want to eat it", thank you and peel it off, and you will have a superb fragrance that you have never felt before. It is said that "It looks like bergamot?" The taste is a refreshing tangerine. If you rub the skin like an eggplant and cook it, it will be delicious. Phantom Keraji oranges, please feel the scent once you see it."
https://www.orange-garden-inc.jp/sommelier/mikan-introduction/"Hanaraji Village is a small village located in the southwestern part of Kikaijima.
Sightseeing
The highlights of Keraji village
Haraharu oranges
The settlement of Hanaraji is also known as the birthplace of phantom mandarin oranges and mandarin oranges, and the season is from September to December. The mandarin orange is characterized by its unique and elegant fragrance, and its functionality is perfect, but it is also useful in local Kikaijima as a phantom mandarin orange that is small in volume and difficult to grow. It is not unusual for the island to be difficult to obtain, and it is traded at a very high price due to its uniqueness and rarity. "
http://kerajihouse.moon.bindcloud.jp/pg344776.html花良治集落 automatically translates as "Hanaraji village" but interestingly the Google translate also automatically seemed to recognize the "Hanaraji" component as "Keraji", and the name Keraji also appears in English form on that site. I don't know, but I suspect this could mean that "Hanaraji" actually should be "Keraji" in this context. The characters might refer to an older name, rather than the standard Japanese one for these characters.
Or maybe it could just be that Hanaraji is a more specific place within Keraji village?
"If you walk in the village, you will find a stone wall of a fence and an old narrow street. In the garden of a private house, you can see tropical plants and native citrus fruits (Kerajimikan ケラジミカン, Kuriha クリハー ( Kikikai Mikan 喜界島みかん ) , etc.) unique to the village of Hanara "
These are the same characters that refer to Kikkai mikan, so there's no doubt that "Kikikai" is just a different spelling for "Kikkai" here. Kikkai mikan was identified as one of the parents of Keraji mikan in another DNA marker analysis, which we are not going to elaborate on here.
This may be another source of interest, relevant to Japanese varieties in this specific area:
http://www.japanfruit.jp/Portals/0/images/fruit/endemic/pdf/mandarin1.pdfEnglish translation here:
https://translate.google.com/translate?hl=en&sl=ja&u=http://www.japanfruit.jp/Portals/0/images/fruit/endemic/pdf/mandarin1.pdf&prev=searchEdit: I found out why google translate may have recognized Hanaraji as Keraji.
This source seems to indicate that Hanaharu mandarin (or Hanaryoji, as would be rendered by the translator) seems to be somewhat synonymous with Keraji mandarin, and Hanaharu uses the same exact first three characters in Hanaraji village.
" ケラジ ( 花良治 ) "
https://www.flower-db.com/ja/flower:687There's obviously a connection here, but I'm not sure I'm able to untangle it for sure.