As WellFooled said, I believe they went over this during the Tokyo Fan Fest when the new dungeons were announced. Presumably they designed the new to 2.0 dungeons with the idea of hard mode versions to be released later in mind, but the dungeons that existed in 1.x obviously were not designed in such a way. All I can imagine is that for the 2.0+ dungeons they actually had more assets and paths set up upon release that they later used for the HM versions, whereas there was nothing unused in the 1.x dungeons to draw from, so completely new areas would have to be made and somehow incorporated into the overall design of the existing dungeon.