I think i've got a little more of this picture.
I can't figure out what you are trying to do, or what you've done. You keep posting segments of pins_arduino.h and variant.cpp, and never the code that you've actually written...
pins_arduino.h and variant.cpp are the modules that translate from the names that the Arduino environment uses (1, 2, 3, PIN_LED_13) to the addresses used by the CPU internally. They have nothing to do with "direct port manipulation" except as way to identify which Arduino pins match up with which ports and bits.
The Arduino pin numbers are small and consecutive integers, while the ports are large 32bit addresses, and the bits are bit numbers. In the Due implementation, the Arduino pin number is used as an index into an array of structures with various information about the pin/port/bit/function. In the MEGA implementation, the pin number is used as an index into various parallel simple arrays that each convey part the same set of information. It's part of the power of the "variant" code setup that two different boards can have substantially different implementations.
And yes, to do direct port manipulation, you give up a LOT of the flexibility that you'd get from using the Arduino pin names.