I can wire it pretty quick and easy to alternate coils. I'll usually have a push/pull that cuts them, and then another, or a mini toggle that "flips" them just by switching the coil cut ground to the respective hot on the switch. I agree with Jester about the output difference being from the string movement. The quack factor is individual. A strat bridge pickup angles from near the neck side on the low E to the bridge side on the high E, so it's kind of like saying "which string section are you trying to emulate the strat sound from, low or high?"
On the neck pickup, I find it to be essential which coil you use. Perhaps on a 24 fret guitar it's less apparent because you're already an inch or so back from where a strat neck pickup is. But if you're using the neck pickup as a single by itself, the throaty, greasy sound is only coming off the neck side coil, merely due to its location. As far as the combination with the middle pickup, though, both are okay, because that middle pickup addition notches (or quacks) out those freq's anyway. So you're back to personal preference there.