I can't remember the difference but it was minor that no one cared about. Get the cheaper one and buy a nicer tire with your saving. The stock tires, both hybrid and knobby, should be the first thing you want to change anyway. With $50 saving, you could get nice anti-puncture tires. Trust me, you don't want a flat with this bike - its bit of pain if you don't carry a big wrench.

As for running at 36v. I don't have this bike anymore but I ran it for a season at 36v. The motor does get hot (I did drill the cover for cooling) but it didn't give me any issues. And replacement motor is around $50 anyway.