Ok, I think you're not seeing my point. Earthquake literally offers the one thing that Surf / Waterfall hits and so much more, and the facts are that Surf / Waterfall overlaps in targets with EQ, which is solely PDon. You see, moves such as Surf / Waterfall in a vacuum offer an opportunity for something that cannot break past a specific Pokemon the chance to without interfering in terms of movelots. Take Tyrantrum in RU for example, who literally cannot have a 100% chance to break through Gligar without Ice Fang, but since none of the other coverage moves it offers can hit Gligar hard other than Outrage, Ice Fang is a very acceptable choice, as it allows Tyrantrum to get past one of the tier's most potent support Pokemon. However, Rayquaza has Earthquake, which allows it to bypass Primal Groudon while hitting the Steel-types that resist Dragon Ascent, which means that it literally does the same job as Surf or Waterfall in addition to actually helping out Rayquaza with the things that can take its main nuke. Yes, Primal Groudon is a fantastic Pokemon, and yes, Surf or Waterfall can OHKO PDon, but if you have Earthquake (which means PDon can't even switch into you in the first place), you are essentially wasting a moveslot on a one-minded solution to take down something you already offensively check in the first place. And then, if you do slap in Surf or Waterfall on Ray, you essentially lost an important moveslot to help you effectively deal with a large portion of the offensive or defensive metagame (any of Fire Blast or EQ on Mixed sets, ESpeed on both SD, CB and Mixed, and Dragon Dance on SD), which is something that Rayquaza does not appreciate in the slightest. Also, using SURF on an SD set is literally counter-intuitive to SD Ray's purpose, which is to wallbreak with PHYSICAL MOVES. I can completely understand the slight effectiveness that running Waterfall on an SD set can merit, but fucking SURF? That's completely asinine considering Rayquaza can immediately OHKO defensive PDon variants with a +2 Waterfall while not hitting like a pansy on anything else.
tl;dr pls don't use Surf on Rayquaza pls (though if there is even the slightest of niches, use Waterfall on CB and SD instead)