Why would a rough in pipe be under the concrete?
If I had to guess I'd say that the builder expected the wall to pass over that point, and the vanity installed adjacent. You appear to have built your wall tight to the furnace, which isn't ideal for maintenance reasons. I'd bet that if you had set a wall 12" from the center of the 3" pipe it would line up with the 2" pipe. 

As to why it's under the concrete... the plumber simply used too short a stub. Maybe he had a scrap laying around and wanted to use it up.