They all are born before 1999, so the use of the name is not derivated from the game, obviously.
In Spanish, its use seems to be tied to Peru, basically, and I think that the name was originated by linguistical confusion. In Spanish speak by Quetchua speaking people, and Peruan and Bolivian Spanish in general, the sounds E and I are often mixed up, so the name Efraín sometimes is found as Efraén; this form Efraén can be easily understood as Efrael, because a lot of Biblical names have the ending -el:
Efraín > Efraén > Efrael
The use of the new respelled Ephrael for girls in a science-fiction game can be due to appeal of some Tolkienian femenine names ending in -el as Galadriel, Tinuviel, Berúthiel, Lothíriel... Yes, the Tolkienian ending is -iel, but perhaps the game authors pronounce similarly -ael and -iel (I don't know because of my poor knowledge of English pronunciation) or simply they have assimilated -el to an feminine ending sound (in addition to Tolkienian names, there are the French pronunciations of Gabrielle, Danielle, Michelle...).