Mara,
Others should be able to correct me but the issue with the fat in supermarket dried milk is more of a 'stale' flavor than shorter shelf life.
It seems that commercial manufacturers have access to better dried milk than what we do in the regular food stores.Roller dried milk is hard to come by and spray dried milk is what most people use. Some sources like Beckett mention the benefits of using milk crumb, but that is also a sophisticated and complex process because it starts with wet milk.
If you look at commercial chocolate ingredients you will see that they sometimes mix the nonfat milk with whole milk. I guess an added advantage of using the ghee is that you can control the amount of fat very precisely.
I didn't get back to testing other formulations with the regular whole milk but if you have more than one machine you could try it and taste them side by side.
Felipe