Yes, the stones are drawn on the board’s canvas element using Javascript. That’s why I made a Tampermonkey script instead of just custom CSS, they “monkey patch” the draw stone code:
GoThemes.white.Plain.prototype.placeWhiteStone = placeStoneFn(white);
GoThemes.black.Plain.prototype.placeBlackStone = placeStoneFn(black);
I’m going to try to adapt Adam’s work for custom boards and make a proper pull request for custom stones… Adam also suggested easy buttons for one color go and blind go, I’ll see what I can do