In continuing a theme of talking to myself...

It looks like the GD::Graph has a few experimental methods that might do what is desired here:

$graph->get_hotspot($dataset, $point) 
Experimental: Return a coordinate specification for a point in a datas
+et. Returns a list. If the point is not specified, returns a list of 
+array references for all points in the dataset. If the dataset is als
+o not specified, returns a list of array references for each data set
+. See "HOTSPOTS".

$graph->get_feature_coordinates($feature_name) 
Experimental: Return a coordinate specification for a certain feature 
+in the chart. Currently, features that are defined are axes, the coor
+dinates of the rectangle within the axes; x_label, y1_label and y2_la
+bel, the labels printed along the axes, with y_label provided as an a
+lias for y1_label; and title which is the title text box. See "HOTSPO
+TS".
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Perhaps with that I can then get coordinates with which to pass to the polygon and then apply to the image.