Flower Tree World puts Minato to sleep, then Madara spams black rods along with the chakra chains manifested to suppress Kurama's power. Minato is restrained and in the process of dying once Kurama is extracted.
Manifesting an avatar would not be in Minato's favor against the rinnegan. He'd be an easier target to hit. There is no definitive proof that sage mode Madara's reflexes supersede BM Minato's own. To actually catch him or hit him, he'd probably have to resort to Shinra, Bansho, or Rinbo.