Andrew,
Great question! I’ve been involved with Tsugaru Shamisen and the whole scene both here in Japan and abroad for just about the past 11 years or so. Instead of giving you a proper text book answer I’ll simply relate to you my experience with Tsugaru Jinku and you can make of it what you want.
Back in 2002/2003 I was taking lessons from a Minyo accompanist who also knew Tsuagru Shamisen. He first taught me Tsugaru Jinku in Honchoushi. A few months into the lessons he asked me to play at his house party/get-together. After playing Roku Dan/Jongara bushi, someone in the audience shouted out “Tsugaru Jinku!!!” immediately my teacher launched into Tsugaru Jinku leaving me in slight bewilderment because at that point our Shamisens were still tuned to Ni Agari.
Later I questioned him “Isn’t that song suppose to be in Hon Choushi!?” He turned and glared directly at me with a look of disbelief as if that question itself was so utterly meaningless as to actually catch him off guard . Finally he responded in his thick Northern Japanese accent “Well, what the hell is the difference, it’s the same song right!?”
A few years later I was sitting in a park playing Tsugaru Jinku in ni Agari . Several members of a local Minyo club (both young and old memebes) walked by. They came over to listen to me for a while and I could hear them babbling amongst themselves “Oh he’s playing Tsugaru Jinku! Wow! And look, it’s Ni Agari! Hmmm. Interesting! He plays it in Ni Agari! Woa! How cute! Yes, that’s really neat-o! We play it in Hon Choushi right!? Yes yes! We certainly do!” and so on.
And again some years into the future I found myself at the annual Tsugaru Shamisen tournament in Hirosaki city. I approached a group of younger players who were sitting outside jamming. I could tell they were all in Ni Agari! I asked to play with them and they said they were going to jam on Tsugaru Jinku. Once again, Ni Agari tuning. They didn’t even seem to give it a second thought.
So it seems that in the end it doesn’t really matter all that much. No doubt it was originally conceived to be played in Hon Choushi but I guess the idea that it might be an issue in Japan (or anywhere) has become the equivalent of asking someone at a resteraunt about using a lacquered chopstick as opposed to an old fashioned wooden chopstick. They’ll just look at you like “Well, either way the food gets in my mouth right!?”
Hope that helps to shed some light on this issue!