My 10cm Nitto quill stem meaures about 104mm from them center of the stem bolt to the center of the handlebar. Not sure, but I believe that center-to-center (C-to-C) is the correct measurement. However, I can't explain the extra few millimeter.

Edit: I'm measuring along the top of the stem. If I were to measure along the side of the stem, the result should be closer to the noted stem length.