I think it could definitely work. One problem with it though is that it lacks the speed boost from Dragon Dance, so maybe a Choice Scarf would do better.
Obviously, Geomancy Xerneas is taking it out, but Geomancy Xerneas takes everything out.
I do agree, the surprise factor of Special Rayquaza will catch opponents off guard. Usually Rayquaza likes to use D-Dance a few times before attacking, so when your opponent prepares for set up, just hit them as hard as you can. I quite like that strategy, it works well against Defog users.
I also like the set. I think it would work quite well against Pokémon common in Ubers, like Yveltal, which likes to carry Sucker Punch and Special moves, so usually the EVs are split into Attack, SpAtk, and Spe, meaning that it won’t have bulk investment a lot. Based on that information, here are the calcs:
252 SpA Rayquaza Thunderbolt vs. 0 HP / 0 SpD Yveltal: 224-264 (56.9 - 67.1%) -- guaranteed 2HKO
So, it can 2HKO Yveltal, with full investment in SpAtk. Not too bad, if you ask me. Of course, Sucker Punch it really dangerous, 2HKOing Rayquaza with priority (well, my personal set for Yveltal does that):
48 Atk Life Orb Dark Aura Yveltal Sucker Punch vs. 4 HP / 0 Def Rayquaza: 187-222 (53.1 - 63%) -- guaranteed 2HKO
So, that’s just a comparison between Yveltal, a common threat in Ubers, and Special Rayquaza. I think, personally, you should run a Scarf and Modest, for the extra power and speed.
So, overall, I think that set will work in Ubers, definitely, just maybe tweak it a bit. I think that Special Rayquaza is very underrated, there are reasons for that, but I think it could work just as well as a Physical variant.
Hope this helps! :)