At the moment, RawTherapee only allows raw images with the same dimensions to be used as flat-field images. Your best bet is to convert the flat frame into a DNG. There is a thread discussing the creation of synthetic raw images. One of the comments links to this RawPedia section that shows how ExifTool can turn a tiff into a linear DNG. I think it’s possible to create a mosaiced DNG by setting the right tags (probably “CFA” or “Color Filter Array” for PhotometricInterpretation, your camera’s value for CFAPattern, etc.).