Edit: For context, the page that is being discussed is linked here.
Legitimately, you can only get QR codes from a Pokédex of someone that owns said shiny.
Since the given mon is shiny locked, no one can legitimately have the QR code, thus a shiny dex entry would be illegal.
Ninty/GF probably don't care. Probably.
Tho it isn't new for them to restrict people's access due to illegitimate dex entries; back in Gen 4, before the Arceus event, anyone with Arceus dex entry could not get onto the GTS.
The game does not generate QR codes for certain UB/legendaries, as you've explained. As for why the game can't be bypassed to generate them, I simply don't know.
The game reads Gen 7 UB/legendary QRs just fine. If you could get your game to run in JP 3DS, you'll see that it can scan these:
https://projectpokemon.org/home/gallery/album/809-special-pokémon-jp-consoles-only/
Not sure you'll ever hear a positive response relating to this. As far as I know, only one guy made it, and no one else seemed to have cracked the code (publicly), and I've not heard anything about these. Also, interest has died down so I'm unsure we'll hear anything about this
Also I think converting the QR to hex then back won't work. I believe it needs some kind of decryption and encryption so can't make them via simple hex editing.
Edit: Info I could find related to signing the QR.