I'd ask your local support team for a steer on that. My take is that if you go in and change any of the code, the result is an unsupported system. There may be other ways of tailoring SS, but the only ones I know about are colour schemes and logos.
For one of our clients we replaced SS with hand built code and calls to event manager/opentouch. They wanted to get an exact match on look and feel and were thus OK with this approach as it gave them all the control they wanted. However there is an ongoing cost for doing something like this.