I think that although it might not be 100% clear cut whether the embedded fonts issue on a body tag is a bug or a missing feature, one thing that is certain is that many people do not consider it a total show stopper. I hope Kobo do fix/implement this in the future but I didn't notice a huge problem when I was reading the Larsson books (this is not to say I don't care about typesetting, one reason I prefer using LaTeX over the more usual word processors like Word is because of the much nicer typesetting).
Also vis-a-vis the matter of principle, publishers designing things exactly as they want
- this will simply never happen with ePub, ePub was not designed for this. ePub was designed to reflow, reflow means typesetting needs to change. PDF was designed for creating documents which are exactly as designed, but as many-a-ereader-user knows, PDF are not ideal for ebooks since the size of the devices and preferred font-sizes require reflow.