I just think that when the ep "Grampa vs. Sexual Inadequacy" was first released, The X-Files wasn't nearly as famous as the show would become in later seasons, ergo the soundalike version of Mark Snow's theme music. By the time "The Springfield Files" aired, The X-Files had become one of Fox's most popular shows, hence not only the use of the actual series theme but the guest appearances from David Duchovny and Gillian Anderson.