I see, you've done homework :-) The thing, we agree on, there are many posibilities (plus guessing involved) -not to mention crop issue, which I didn't think of yet.
Because of that, inside GUI, there won't (can't) be every possible situation taken into account -in special cases, user would need to rotate images (before embedding) as needed. No big deal, I think.
Anyway, I'll try to support workflow as from DPP in first place, because of many reasons, e.g:
-it's Canon's official (and free) software,
-it's the only converter, which preserves all metadata (exif+makernotes,iptc and xmp) when converting to JPG/TIFF,
-after all, we are embedding something into Canon original file!
-and finally: DPP is my favourite converter :-)
I'm quite sure, it will work for most normal cases. Now, where do I get time to do something?..
Greetings from Slovenia,