MSSCCI Control Panel manual configuration
Accepted answer
This is a really late response.. but can you clarify on what client-side properties you want to change?
The MS-SCCI control pane is backed by an xml file on disk which stores the properties... although it's not officially a supported workflow to use (vs using the GUI) it would be possible to modify those files by hand (or have a script written) to change the property values there. For example, see the many *.pref files located in this directory:
C:\Users\<user>\AppData\Roaming\IBM\Rational\Team Concert MsScci\preferences