I found the source. It’s here: processing/java/src/processing/mode/java/Commander.java at master · processing/processing · GitHub
It seems like there is/was a --preferences= argument planned that allows to
pass in a prefs path if that was specified
but the code is commented out. At least, for now, it doesn’t seem like there is any other option other than modifying preferences.txt directly. I think it would be a good option though. In my case, I don’t like to make these changes permanently.