Ryan’s tramming tool clips onto the nut, not the endmill, so it turns with the spindle and measures the axis of rotation, not the shank of the tool or crookedness of the collet. As long as the spindle is one rigid assembly it doesnt matter where you attach, you always sweep a plane perpendicular to the axis of rotation.
If you inserted a smooth rod into the collet and had an arm that slipped around the rod like a plain bearing and you ensured the spindle didn’t turn, then you would be measuring the axis of the endmill/collet.