The sensor-on-each-side method (break-the-beam) will have longer operating range by a factor of, say, 10 or more. Just angle the beam diagonally across the track (rather than perpendicular) so that you don't get intermittent gaps between cars. Also, since you have to remove 1 of the 2 components, make the emitter (clear bulb) the more distant one...this improves sensitivity in that the receiver component operates at lower currents and is more sensitive to noise pickup from the extended wiring.
Yes, you could simply reverse NO and NC. You could also use a relay module that has hi-level triggering on each input. Most eBay relay modules now offer select-able hi or lo level triggering by moving an on-board jumper. Power may not be an issue but if you reverse NO and NC, then the relay is normally "on" drawing coil current when nothing is happening. On the typical 5V relay module the blue Songle brand relay that coil draws about 1/2 Watt when active. So you are burning that much power in the idle state; again perhaps more a philosophical issue than a practical one but worth mentioning.
Perhaps obvious but the ITAD timer is both for accessory delay AND to deal with the short inter-car gaps when using the reflective method. So even if using the reflective method you might want a small delay to keep the relay triggered between cars or during the time that a dark car goes by.
If you can configure a break-the-beam system you should get bullet-proof performance.
The 4th pin on the modules is to let you turn the emitter on and off; it might be labeled EN for ENable or DI for Data In. Pulsing the emitter with digital codes is how your TV IR remotes work. In occupancy detection you would just connect this pin to which polarity keeps the emitter "on". The type A module I showed above even has a jumper on board which you can install to keep the emitter on so you don't need to make a separate electrical connection to the 4th pin.
I think I got all your questions! 
