I must say I was a bit curious then reading at Stockholmviews.com the the sharpness of the Canon 8800f flatbed scanner can be improved a lot by placing the negative directly on the scanner glass plate. And yet even better when taping the negative to the bottom of the glass plate (inside the scanner)! I have not tried to place the negative inside the scanner itself, but this morning I did some comparative tests with one negative using the OEM film holder and the glass plate. I find similar results as S.R that better sharpness are achieved using the glass plate directly.
After trying this, I remembered that Canon did indicate that they recommend that the negatives are scanned emulsion side up (I would normally do it with the emulsion side down). Then the two methods are even closer (but still with the better result with the negative directly on the glass plate.