After thinking about it a bit, I decided to move control of the amplitude of the control gene effects into the control gene itself. Since the amplitude of the changes made to the component genes is a property of the expression process, this seems to make the most sense. As part of the control gene, it will be subject to mutation, and mating when I introduce those processes.
Different control genes now may have different amplitude effects. Nothing else is changed: I create a single genotype (which I was calling a chromosome tree), with three chromosomes. Each chromosome consists of one control gene and four component genes. All codons are randomly set within their ranges for each drawing. The amplitude determines how much the control gene can modify the original codon value each time it uses the component gene to express a shape.
Shapes remain restricted to rectangles and ellipses. Colors are restricted to grays. This series can be seen by following the link on my Experiments with Evolutionary Art page.