Yes, but there are two limitations:
1. Don't edit isolinux.cfg with a windows editor, unless you know exactly how to preserve Unix text format.
2. You cannot simply write to the iso file. Instead you have to copy the files from the cd to a temporary folder, edit isolinux.cfg and create and new iso file with mkisofs. Take a look at the remastering article in the wiki. It explains how to modify the cd and how make a bootable iso file that contains your modifications. The only difference is that you don't even have to remaster because you can copy the KNOPPIX image file right from the cd without uncompressing it.