Well, you said you didn't want obvious red barcode scanning light. You wanted non-powered/passive ID for each car.You were worried about identifying the start/end of barcodes/optical things on cars.Adafruit is not the only source for tag readers.If something else comes to mind I'll put it up here.
Only the detector needs a tube if that. Put it behind an aperture. In the mid-80's at a Trenton Fest I saw some guys who made a scanner out on a dot-matrix printer. They mounted the light sensor in a pointed pen barrel and got recognizable images. The IR is just for illumination.Depending on train speed you may be talking 1" long strips. You might try printing flat black stripes on silver reflective material and see if they have that on sticky-back sheets.
IR reflectivity, you might be able to test with a webcam, but might have to modify it.