as far as i can tell, you have to change the value in the fonts settings.
if i look in the API under "Font commands" i can find a getXFontNames (what a terrible name!) but i cannot find a way to set the value.
it should not be hard to add a command for setting the subsetting for a single font...
as an alternatvie, in the pdf "section" you can find a font attribute that tells what is supposed to be embedded: if any of the fonts are not subset, you can warn the user (or create a log file) asking the user / operator to change the setting.