They clash, and the codes to change have been heavily modified by SP. I tried to do it the other way around, and it's basically "modify all the SP files" or "modify all the Single Category" files >>
Single Cat has clashes on;
Subs-BoardIndex.php, Sourses/BoardIndex.php, BoardIndex.template.php (that's because I removed the Info centre) themes/default/scripts/script.js and Sources/QueryString.php
I killed my test site trying to do the edits myself so I can't tell you what the requirements are around the other way lol.