In the classical CAD days the end product of a 3D model in cad often was a set of 2D drawings with the tolerances noted somewhere on it.
However in the age of 3D printing the 3D model itself is the end product. Right now the only way to have hole tolerances is to actually 'hardcode' them in by not model something nominal, but model it with the proper tolerance. This seems rather clunky if you ask me, what if someone 3D printed something with plastic and wanted the end product to be in steel, would he remodel the whole thing with different tolerances?
I opt for a way of assigning tolerances to holes, and where this tolerance will actually be in the 3D model and you can change easily. And if you would export the 3D model to a STL file for printing, the tolerances get included. This way you don't have to manually 'hardcode' every tolerance in.