Generally, you avoid touching them if possible and don't put peripheral register definitions in them, to keep them standard.
OTOH, defining these registers inside include files is rather common, one reason being that they do not depend on the linker you use, and second that you can add attributes for specific memory access (like disable caching, etc.). So even if some definitions look over-complicated, they may (or not) have their purpose, and writing your PIN_* as a define on top of the existing ones with longer names is a better option IMHO.
As for the PIN_2 register, it may contain some pin-specific stuff, like pull-up/pull-down enable/disable, drive strength, open-drain configuration, etc?