Didn't know I had to use the "%s".
Args can be both inside and outside the quotes.
Note that FAF will still need the default game.prefs file even though it uses the settings from the specified file.
Otherwise FAF will give an error which can be ignored but is annoying.
For reference the exact text I used is:
"%s /prefs Game_FAF.prefs"
"%s" /prefs Game_FAF.prefs
(I know from experience how annoying it is when theres an answer to the question but all they say is: 'got it, ty'.)