So, the situation surrounding the different versions of "Madara Uchiha" make systems like that odd. This exact version of Madara is similar to Five Kage Madara, in which they are both able to be used alongside Madara Uchiha Founder. In order to unlock that character in the home interface, you need to have Madara Uchiha Founder, or I believe Ten Tails Jinchuriki would also allow that character to be unlocked.