Well, I did have a synth raid up in Sanctuary and I didn't have my turrets in quite the right place, either. Anyways
I did have an infiltrator. Someone who'd been there a while and I'd even assigned her to a security post. While I was busy popping off the synths in the middle of town, she was down at the bridge, on watch. When her sleeper trigger went off, the turrets turned on her. I later found her "Settler" corpse and, surpise surprise, she had a little synth tech pop out in the gear that was recovered from her.
So, never fear, the turrets may not distinguish between synth and human but they seem to be very good at distinguishing between hostile and non-hostile.