This happened during one of my runs yesterday and it was strange enough that I figured it was worth posting here. My guess is there's a very short window (1 frame?) before the boss starts attacking and Thunderstone happened to hit at that exact moment.

Probably not viable enough to use consistently, but if the stars align...

Yes, sprite's can stun the boss before it's first attack. However, this is indeed a very short time frame and most of the time this doesn't happen. Since the boss is stunned like normal i don't think this is considered a glitch.