I Am Not A Climate Scientist, but here's the EPA's page explaining the three scopes model of emissions.

https://www.epa.gov/greeningepa/greenhouse-gases-epa

(IMO the MS post does a better explanation but this is obviously a more reliable source)

I doubt anyone counts indirect use of a general purpose tool, but hey read the link and you tell us.

How would one even begin to track that?

I assume MS has records of how many licenses they've sold (not much they can do about pirated software). They could come up with an estimate of how long a particular OS was probably used on average and calculate how man licenses were sold times how long they were used and then convert that amount of energy use into carbon credits. It's not perfect, but probably good enough.