I assume that you are converting raw images from a DSLR camera. The input hint "raw cfa" will overrule the RAW Format Preferences. If you don't want that, delete the input hint (then the RAW Format Preference will apply) or replace the input hint.
Caution! When using the BatchFormatConversion script, the Bayer/mosaic pattern will NOT be stored in the FITS file.
When using the input hint 'raw cfa', the resulting FITS files contain the color information because they are CFA images. In order to convert them to RGB you will have to debayer.
The list from the link that Rob provided is probably outdated. An up-to-date compilation is available for different formats in the following way (cited from
https://pixinsight.com/forum/index.php?topic=11281 ):
"The FormatExplorer window provides complete information on file format hints for all supported formats. Select a format on the left panel, then double-click the "implementation" item."
There is information for FITS, JP2, JPC, JPEG, RAW, TIFF and XISF format.
Bernd