So the right way to handle the carbon accounting isn't to assume that all the CO2 produced by the refinery processes count against the hydrogen produced, but rather that the energy that refineries get from burning the hydrogen would be replaced by them burning natural gas instead.
The per-kg energy value of burning H2 is ~2.5x the value of natural gas (refineries generally use LHV for this accounting). But each kg of natural gas that gets burned produces ~2.8 kg of CO2 (because burning replaces the puny hydrogen with relatively larger oxygen atoms).
2.5*2.8 = 7kg of CO2 per kg of H2 taken out of the refinery. Which isn't as big a difference from the 10kg reported in the article as I expected when I set about writing this comment.