I would say that manual stretching is definitely within the scope of practice of a well-qualified (and certified) fitness professional. (I certainly hope so, I’ve been doing it for years!) However, you don’t want to overstep your boundaries here. If you have a client with orthopedic issues, it’s best to consult with their physician or physical therapist first – they’ll tell you what to do. The last thing you want to do is cause more problems. Like anything, if you’re not comfortable doing it, don’t.
Yes; This is within the scope of practice of a certified personal trainer. They just have to be sure to tell the client exactly where they will be placing their hands, and ask if they are comfortable with that. The personal trainer is also expected to know how long the stretch should be held for to avoid over-stretching that particular muscle.