I know this question was specific to specialty fries, but I had an issue mobile ordering from Pecos bill and trying to add the guacamole upcharge. Kept getting an error and when I went in person to order they said it couldn't be added to a qsdp meal.
So all that to say, it is probably ymmv at each specific location if you can add an upcharge item such as specialty fries. Glad it worked out for OP.