I haven't been designing PCBs for long at all, in fact most would probably laugh at the noobishness of my designs. However, I do have machine shop experience with CNC machine tools and it's normally assumed that a toolpath shown on the drawing or on the machine (very few of the machine we had back when I did this work had graphical displays, not like modern ones) meant that the cut point was the center line and the rest was the tool diameter. SO if you wanted to cut off 100mm length of material, using a cutter with a 2mm diameter, the line had to be at 101mm to result in the finished product having a 100mm length.
Probably not explaining my thought process correctly, but this is also something I learned as a child, learning how to saw wood. Always mark which side is the scrap piece, so you place the saw blade on the proper side of the line so the finished piece will be the size you want, not the size you want less the width or partial width of the saw blade.
It sounds like I am actually agreeing with the OP, however, it is not the job of the Gerber to specify the tool path, but to specify the desired dimension. The CAM software provides the tool compensation to the finished product ends up with the specified dimension regardless of the size of the tool bit being used.