Correct, they just draw lines on the dynamic lighting layer. There is no way to make dynamic lighting only affect some players, it's all or nothing. If you uncheck "see" from the token aura's Player Permissions, and add players to the controlled by property of the token, does that do what you want? Or am I misunderstanding the question? If the token represents a character, you'd have to edit the character's "edited & controlled by" property, as the token will inherit the character settings in that case.