MSSCCI installation
One answer
The official answer is 'no'; there is no way to have this customized when installing MS-SCCI through the Installation Manager.
There might be a workaround though: There are XML based files on disk that are used by the MS-SCCI client-side preferences. In theory you could write a script that would update these files to the 'default' settings you want. Take a look at connectionpage.prefs or repository.prefs (and others) in this directory:
C:\Users\<user>\AppData\Roaming\IBM\Rational\Team Concert MsScci\preferences