I agree with you. I read it cover to cover at the time and felt like a smart ass ("AksHuALLy renewables can't work alone!"), then wondered a few years ago how his calculations turned out in the real world.
1. Sad that he died from cancer
2. Noticed he compared primary energy and felt stupid for missing that
I never got a blanket claim of "actually renewables can't work alone" from the book. It seemed more like "actually you need to understand things quantitatively or you are doomed to talk nonsense".
MacKay's "renewables can't work alone" claim always seemed carefully scoped to the economics of 02008 (when solar modules cost 33× as much as they do now) and also his own densely populated, rather polar country. Renewables were already working nearly alone, at scale, in equatorial countries and more sparsely populated countries; I live in Argentina, whose grid was mostly hydroelectric at the time, and next door to Brazil, where a large fraction of the automotive fleet ran on sugar-cane-derived ethanol, which is a viable renewable energy source (unlike, apparently, corn ethanol).