When the uploader choose an ocuppied file name in Special:Upload form, the warning is relatively inconspicuous and unemphatic. While tutorials, preventive license instructions etc. are very colourful, framed, bold or enlarged etc,, the overwrite warning is in the basic typeface and drowned under the screen, far away from the problematic file name. (Even I myself sometimes overwrite my own filles unintentionally.)
The warning should be more showy, the filled file name should be highlighted as unacceptable and overwriting of an existing file should be specially approved if is really intended.
Or even, overwriting should be definitely forbidden through filling the file name and should be allowed only through the "Upload a new version of this file" link from the file page of the existing file.