It is possible to create custom preferences in Spotfire and make them available in Administration Manager. This can be done using Spotfire Analyst API class CustomPreference:
There is an example in Spotfire SDK (Tibco Spotfire Developer) called SpotfireDeveloper.PreferenceObjectsExampl.
Tibco Spotfire Analyst API reference: https://docs.tibco.com/pub/doc_remote/sfire_dev/area/doc/api/TIB_sfire-analyst_api/Index.aspx
Tibco Spotfire Developer documentation: https://docs.tibco.com/products/tibco-spotfire-developer