I decided to modify the file gpif2model.xml in the projectfiles directory of the GPIF II Designer project. I copy and modified one of the flag signal sections of the file. The modification does not affect the configuration options but it does show up in the graphical represenation of the interface and I was able to verify the results in the header file.
The .xml file is a little complex, there are calculations based on the selected configuration and modifying one place will not take care of all the required modification. I would recommend using GPIF II Designer to generate your required configuration than change the .xml file directly.
That was the heart of the question. I noticed that the signal definitions are easy to interpret. Since DMA flags do not interact with state machine, I figured I was safe. Unless, of course, you know of a better way to produce a SlaveFifo implementation with three flags in GPIF II Designer. I was unable to find an option to add any signals or instructions for copying a SlavFifo implementation so that I can make changes.
The slavefifo GPIF II project comes as a library with the GPIF II Designer (on the left side of the start page). You can save it as editable and use that to make the modification that you want in it.