You can get Identical pick-ups for all positions if you like, and you can solve the output problem by changing the hight of the pick-up from the guitar body (the bridge would be the highest), A lot of people do this.

Other people prefer to get different pickups for each position, so it's up to you and your taste in pickups.

Actualy, if I had a strat I'd like to stay with single coils. You'll change it's straty sound if you get humbuckers. I've never played a hot rail before, but it's a compact sized humbucker and probably your guitar won't sound like a strat with one of these.