Currently we continue to develop the XPS Annotator. In the latest version later (version 1.22), we will add feature to change the color of the highlight annotations on the XPS document. We have made a version that already has the ability to provide colors other than yellow, and now we're testing the stability of the XPS Annotator 1.22.
Finally we can meet many requests that want XPS Annotator can change the color of highlight annotations.