One sub type of graffiti is the Masonic type, left behind by the many stone masons who worked on the site, especially during the major consolidation work in the 1850s.
Perhaps the Freemasons have just been borrowing symbolism common to the masons.
Another thing I had read was that apprentice stone masons in France were expected to visit the Pont du Gard as part of their apprenticeship. This seems to be true, as building trades in France have an unusual "Tour de France" that requires novices to visit different parts of the country to study.
And here is the evidence, written in stone.