Three orientation places can be confusing at first sight... but I see there's a logic behind:
1. Average user (& 3rd party software) should read IFD0:Orientation and everything should be fine -and usually is.
2. Makernotes:Orientation just tell how was camera actually held -regardless of settings.
3. CanonVRD:Rotation is DPP's internal tag -3rd party shouldn't care about it.
Looking at things that way, DNG doesn't offer more (in regard of your issue), IMO. If it does on some areas, then only as long you're using Adobe software. Now you decide :-)
Of course Exiftool knows about CanonVRD -otherwise, GUI couldn't know about this section :-) Inside GUI, you can see this section by choosing Maker button (tags will be listed at the end of the list).
Right now, I don't think about changing something in regard of embedding previews. As you've noticed, there's complicated logic involved -on the other hand, I'm trying to keep GUI simple (and as fast as possible).
For special cases, I advice everyone to use Exiftool directly (by making custom scripts).
If I can express a wish about DPP: would be nice, if DPP would allow to embedd image back to CR2 (where current DPP settings would be used for conversion); meaning: instead of converting to JPG file(s), resulting JPG image would be embedded back into CR2. Now, let us pray...