I don't think you can do it from the Windchill login since the Windchill login doesn't pop up until after Pro/E is started.
You should think about running a batch file and point to the directory that you want PTC_WF_ROOT to be and then point to the ".bat" file that starts Pro/E.
The other idea would be to have different .psf files and edit the last line to point to where you want the directory to be and use that one when you want to be admin.