Using the following code, I set the opacity in the InkAnnotationSettings in a pdfViewer. The opacity is displayed correctly in pdfViewer. However, when the document is saved, the opacity is set to 1 (and of course, this is wrong.)
pdfViewer.InkAnnotationSettings.Color = Color.FromArgb(255, 207, 242, 4);
pdfViewer.InkAnnotationSettings.Thickness = 30.0;
pdfViewer.InkAnnotationSettings.Opacity = 0.5f;
pdfViewer.InkAnnotationCommand.Execute(true);
Also, you can examine the incorrect opacity setting by looking at the annotation passed into the AnnotationAdded event.
Using the pdfViewerCustomTool custom, the opacity is saved correctly if the ink annotation is modified after it is created (via selecting the annotation, and then selecting "Edit" from the popup menu).