Brainiac 1 is not from Krypton, but he’s not originally from Colu either. According to producer James Tucker, “Brainiac 5, in our continuity, comes from the planet Colu founded by Superman's oldest foe, Brainiac.” The source of the quote is from an October 6, 2006 article at comicbookresources.com.
Here’s a direct link:
http://comicbookresources.com/news/newsitem.cgi?id=8558 Tucker could have revised his position on that since Season 1, but I don’t know. The animated Legion has its own continuity thing going on. For all we know, Brainiac could have been constructed on Earth like Amazo.