Wild guess...a decoy at one of their R&D facilities like Tachikawa. Trying to make the Americans think that they a had an intact B-29. Trying to draw fire away from the stuff they wanted to keep.
Another possibility, a full scale model to help train interceptor pilots.
While it obviously couldn't fly, their pilots could walk around studying approach and attack angles, or perhaps dive on it.
Remember too, few has probably ever encountered an aircraft that large before. Seeing one up close would give them a better idea of size and distance while attacking the real thing.
They did have an airworthy B-17 and like the Germans, used it to develop fighter tactics.
I doubt if they ever got their hands on a potentially repairable B-29 that went down over Japan.
Final possibility..the birth of the Japanese model aircraft industry.
A little known 1/1 scale early effort by Hasagawa or Tamiya.