It is not about fingerprint size, it's about fingerprint sizes delta before and after. Take any image editor or paint app. When you want a tiny line, you barely touch the surface of the screen, when you want a bold thick line, you press your finger harder to the surface - I think 3D Touch work the same way, but I will check that to be sure. The reason I doubt is because it could be implemented much easier, no need for extra sensors and stuff. You say fingerprint sizes are different. Yes, but pressure is different as well for different people, isn't it?
Source: http://www.apple.com/iphone-6s/technology/Apple iPhone 6S Technology Page said:Retina HD display with 3D Touch
The technology behind 3D Touch starts with the display, which recognizes the pressure you apply in addition to the familiar Multi-Touch gestures you already use.
Capacitive sensors
Designed to measure microscopic changes in pressure, capacitive sensors are integrated into the backlight of the display. These measurements are then combined with signals from the touch sensor and accelerometer to provide fast, accurate, and continuous responses using a series of complex algorithms.
To my knowledge, Apple doesn't have a history of flat out lying about their technology innovations. Either they don't say anything, or they give accurate information about how they've implemented a feature.