They would fingerprint the reader, and you, to get a rough idea of which finger is a likely candidate. Even an extremely partial print should be enough to narrow it down to 4 or 5. The reality is that all right-handed people hold phones in their left and so use fingers on their right hand. Lefties do the reverse. So it is already down to five candidates ... which might have something to do with why apple picked that number in the first place.
It depends on the size of the phone. My too open/unlock my phone with the same hand that holds it (pattern unlock). But my phone is tiny. As a phone gets larger so does the likelihood that it is manipulated with two hands. Having the scanner below the screen also requires some dexterity when used single-handed, increasing the likelihood that the thumb is the print finger.
