An obvious question about the CDK rendering code is : "Why not scale text with AffineTransform?" So, of course this is possible, and works quite nicely - but there is a cost.
One of the goals of the rendering code is to start from models of any scale, and render them as consistently sized diagrams on screen. By 'scale' here I simply mean the average distance between points. So the CDK layout code might use a distance of (say) 1 between two carbon atoms, but a file with a structure made in some other chemical editor might have an average atom-atom distance of 100. These are unitless values, by the way.
Now, what we could have done was transform the coordinates in the model to a consistent scale, then rendered these transformed coordinates. What we chose to do, however, was to calculate a single transform for the model and draw with this. If you use this transform to scale the graphics object before drawing you get this for a model scale of 10: