It should line up with any die. Sometimes it helps to manually center the shell plate for the first couple of cases, but once the bullet seating station die is actively seating bullets, the entire shell plate should line up as the bullets are raised into the seating die.
However, if the cases are badly “whop-sided” at their base, they may sit at an angle in the shell plate.
However, if the cases are badly “whop-sided” at their base, they may sit at an angle in the shell plate.