My perspective is that it's supposed to be part of the "who is the real enemy" angle that was a part of the later half of the game. There was this constant back and forth as to whether we should focus on Lilith vs Mephisto as the one to destroy. That process culminates in how the ending plays out.
This part is just a reminder to the player that Mephisto is still a force of evil that can't be ignored or underestimated.