Turns out that the ComboChart adds the annotation/annotationText columns to the last series created on the graph - Meaning that the roles were being added to the Bar graph, which does not support annotations in the ComboChart.
The Line graph, however, supports them - So the 'dirty fix' was to have the line series being the last one in the graph:
private ComboChart.Options createComboOptions(String title) {
ComboChart.Options options = ComboChart.createComboOptions();
Series bars1 = Series.create();
bars1.setType(Type.BARS);
options.setSeries(0, bars1);
Series bars2 = Series.create();
bars2.setType(Type.BARS);
options.setSeries(1, bars2);
Series line = Series.create();
line.setType(Type.LINE);
options.setSeries(2, line);
options.setIsStacked(true);
return options;
}