I apologise, I was mistaken about that; must have been a brain fart or failing memory. Just tested with RC9.3 zip that I still have and it indeed reads from C:\Users\sterretje\.arduinoIDE as shown below and not from the installation directory.
FYI, you don't have to restart the IDE after a change in .clang-format; it seems that the file is read when you use auto-format. Saves you some time restarting the IDE 