its like the other comment said, but my theory to exactly why it was Siennas Sion reincarnated into is because Sion’s wish had layers. These aren’t directly confirmed except for point 3
1) He wishes the stigmata would go to someone worthy of it. However, to God, he is the only one worthy of it, and to the eyes of the people, the Holy King is worthy of it.
2) He wishes everyone, including Pavel to be happy. (this is a theory—>) But God creates miracles, not reality, so it’s possible he was put into Siennas’s body because it’s the miracle that will lead Sion to be able to make both Pavel and the nation of Zeon happy/at peace
3) The forgotten layer: He wishes for “Sion” to not exist. So “Sion” the body ceases to exist, but the essence of the person continues to exist in “Siennas”

Why did Sion reincarnate into Seinnas' body and why does Sion's original body no longer exist?