Exiftool is invoked from FITS via a Perl command in the class Exiftool.java (edu.harvard.hul.ois.fits.tools.exiftool.Exiftool.java)
We have no experience with what you are trying to do. However, here is a suggestion to try. It looks like from the link you've provided you'd like to add parameters to the exiftool executable to modify the output format. In the class Exiftool.java around line 110 you will see the addition of parameters. Perhaps you could experiment by adding your desired parameters to this location of the code then rebuilding FITS. We would suggest forking the GitHub repository first.
Good luck and let us know how it goes.