Just noticed something cool, it seems like the character that serves as the stage III midboss/boss changes depending on...something.
Like when playing as border team, either Marisa or Yuyuko may show up as the midboss. When playing as Marisa-Yuyuko, either Reimu or Yukari may show up as the midboss.
Even *stranger*, though, is for bamboo forest team. At least in practice mode, I've had runs where border team showed up and other runs where Marisa-Yuyuko showed up as both midboss and boss. The actual boss fight has a chance to completely change!
I'm not sure what triggers the decision or if it's truly random, but it's something to investigate.