It is also a foreshadowing of Jesus’ death. Mary lost her Son for three days not once, but twice — once when He remained in the Temple, and once when He was in the tomb.
When I pray this Mystery, I like to pray for those who have lost Jesus in their lives, that they will find Him again in His Church (temple).
I agree that it can be a difficult one to understand. If you have a hard time with it, you are in good company. Recall that Mary and Joseph did not understand it either (Luke 2:48–50):
When his parents saw him, they were astonished, and his mother said to him, “Son, why have you done this to us? Your father and I have been looking for you with great anxiety.” And he said to them, “Why were you looking for me? Did you not know that I must be in my Father’s house?” But they did not understand what he said to them.