the INDI Gphoto driver uses the libgphoto2 library to communicate with the DSLR.
Setting the camera's SD card is basically the same as e.g. using the command line tool and setting:
gphoto2 --set-config capturetarget=1
That is, the RAW or JPEG image is not leaving the camera via any USB out, but is directly stored on the camera's SD card (when inserted) when taking an image or movie.
So saving the image in FITS is not possible when setting the target to SD. To save the image in FITS format, the RAW camera image first has to be read out from the camera
via USB (e.g. on Rpi or any PC) and then converted to FITS format. Once converted to FITS format the FIT headers are set.