DVD

Kakashi couldn't destroy the Gedo Statue's head because of its durability. It could be the same issue occurring here.

Madara's true power was never explicitly shown or explained. What was seen during the time-reversal sequence was more of a representation of how overwhelming his visual prowess was.

Minato made it by copying the tailed beast bomb.

The Nine-Tails can manipulate the host’s chakra as long as the seal is weakened enough, which it is in this case. This has been shown multiple times. A good example is when the chakra arms moved on their own or when it was able to form a Tailed Beast Bomb. Additionally, it could possess and manipulate the host like a puppet—such as during the Fourth Great Ninja War arc—where it occasionally spoke and attacked through the host.