It is possible to recruit a second Roufas in Emelia's Quest. Normally, during the course of Emelia's Quest, Roufas stays at the Gradius HQ, and gives you your missions. But you can recruit another Roufas in Ancient King Mu's Tomb in Shrike (the same place where you'd recruit him in any of the other quests.) So, there's one Roufas in Gradius HQ and there's another in your party!
Taken with permission from Flying Omelette.