Just to add another wrinkle/line of speculation, how about Hermione's work/McG's gift for the LP? Pretiosissimum Donum Dei translates as "the most precious gift of God" and is an important alchemical work, according to this site. Wikipedia calls it Rosarium philosophorum sive pretiosissimum donum Dei ('Rose-garden of the philosophers, or most valuable gift of God'), assuming that the same work is referenced. In either case, it appears that the illustrations are the most famous part of it - poor Hermione, handcopying them.

Anyway, drawing from the first website: This famous work has a series of flasks in which the evolution of the white and red stones is described. Is the LP on the trail of a more different Philosopher's Stone?