Alright I updated to 1.3.1 and if the second post is deleted (with no more posts ahead of it) it doesn't go above the first post, maybe this is an issue due to me also have a double post merge add-on, but it seems to be sorted out now.
Indeed @Brogan, I performed a few tests and it seems the add-on creates such behavior.
Thread first post is posted
Second post is posted
Second post is soft deleted
Thread starter posts again, #1 and current post is merged
Deleted post is above first post since the "time" is changed and the first post comes down
I guess its intended behavior with the add-on but I was seeing it the first time.