Hi Mark,
Linkouts are set in cytoscape session properties, not in the xgmml. Here's how they work:
These ultimately are stored in a linkout.props file, which you could programmatically write and package with an xgmml in a .cys file (a zip of session files). You can unzip a sample .cys file to see all the components, then just replace the linkout.props and xgmml.
- Alex