Both have their good and bad points - the layered templates produce a very integrated character, with rank inherent in the template, but suffering from the possibility of characters looking much more alike than is perhaps desirable; while the SC3 method takes longer and is somewhat more erratic, but the chances of any two characters coming out anything alike are virtually nil.
I went with the SC3 format, mainly because this game should be usable as a drop-in setting for any SC3 character to play in. Klax and I took the list of professions from SC3, and first pruned it of anything that would not be important in The Necklace, then added in new stuff peculiar to the setting. For example, in the Necklace, Shields - reflective shaped plasma fields and defense lasers - are not very viable, so they are dropped, along whit anything too military; While we added Xeno-Archaeologist for those who study the ruins of the Builders.
Then Klax and I took a look at how these professions would fly with the various playable cultures/species in the Necklace, and marked them appropriately, so a profession marked A, R, C would be suitable for Altiplanian, Rasi, and Carnivales characters. This is not meant to be a block, but a guideline. A player character can have any profession the player wants, but you won't find NPCs of non-indicated cultures in that profession.