PDFE uses the regional settings on your computer to determine what the "list separator" (i.e. comma vs. semi-colon) will be. In languages where the decimal point is a comma, the standard is that the defined list separator is the semi-colon., so you only need to change that character in your Windows regional settings to a comma, and the decimal separator to a point. Take note this will affect globally other programs that may use this Windows settings.
When the csv files are generated from the PDFE web interface, the list separator is the defined in the [config] section of the language file being used by the web interface. You can change it editing that language .lng file, that you can find in the Lang subfolder where PDFE is installed.