What is the significance of primary and secondary flats in wafers?
There is no physical relationship between flats and the orientation or doping of the wafer. It is purely convention.
The primary (large) flat indicates the orientation of the crystals, and, if present, the secondary (smaller) flat indicates the doping.

The numbers in braces are the Miller Index of the crystal orientation.
This convention is only used on smaller (&lt; 200mm) wafers. Larger ones use a notch to indicate the orientation and do not include doping information.