Hi Bogdan!
Thanks for detailed description. You give real help.
It is terrible that we have 3 places to keep information about orientation! Now I understand why Adobe promotes the DNG format :) But I am not ready to switch to the DNG and still hope to optimize workflow with CR2 files.
You have told about CanonVRD section. Can Exiftool see this section? If yes, it will be usefull to sinchronize all information. If no - of course it can be manual work only. Of course, it will be better to introduce all this things inside DPP. But I doubt that Canon will do it.
May be it will be usefull to add in GUI the function of manual embedding, when we can see both CR2 and JPEG and can decide how to rotate image. But it can be labour intensive.
Anyway, thanks a lot.

All the best,
Igor