I started a game this morning and managed to recruit an NPC with the "Royalty" background (+100% prestige).  As far as I could tell, her trait did nothing.  No effect from just having her under my command, without more; no effect from stationing her in my city; seemingly no option to apply the bonus to the city (like a "reside in city" command or some such); and it appeared that marrying her didn't help either.

On the other hand, when I started a separate game and created a sovereign with the "Royalty" background, his prestige multiplier worked from turn 1, whether he was in my city or not.  And, for the NPCs I've found that have some other trait which provides a fixed benefit per turn (like "Merchant"), I have had no problem getting these benefits.

Does anyone know if there's something I'm missing?