I've never seen any documentation on Preferences.tps except for the color palettes. I suspect there is more that cane be done, so if anyone else has an answer on this one, I'd love to know!
I asked the same question a year ago, and got no response from any of the Tableau folks. I suspect there are other things that could be set in this file, but without knowing the syntax we're sort of out of luck.
I remember seeing your question. It sure would be nice to know...
Not the answer, but confirmation of more possibilities in the file, and related syntax that could be a starting place:
<preference name='text.font.nofontfallback' value='true' />