Toho's International Dept renamed the movie ATORAGON for foreign sales. When AIP bought the film for the US, they shortened the name to ATRAGON.
I've never seen an official reason from Toho for the change. There has been speculation that the name was derived from ATlantis dRAGON, but the name clearly refers to the submarine, not Manda (who is barely in the movie and wasn't from Atlantis). Here's a Toho international sales sheet for the movie: