It's been a while since I read the paper, but IIRC, you are wrong about how the process works. First I'll define some terms:
Image pixel: pixel in the final image
Sensor pixel: actual pixel in the sensor
The microlens array bins several sensor pixels into single image pixels. Depending on the incident angle of the light on the microlens, the light will go to a different sensor pixel. This means you can adjust the aperture, as well as focus in post-processing, since a narrower aperture just means a pixel is illuminated by light from a narrower possible number of incident angles.
If I had a whiteboard, I'd draw you a diagram, but you sound like a knowledgeable photographer so you probably "get it" if not, just look at the ray-diagrams in the depth of field section of a photography book.