Ho-Oh and Lugia are above everything bar Karen's Houndoom and Bruno's Machamp when you catch them. You also have more locations to beat before you get to E4 in HGSS giving you a chance to reach even higher level. Heck, even higher than champion's Pokemon.
Steven can't deal with Groudon. He simply can't. Lance doesn't stand a chance against Lugia if you decide to teach it Ice Beam+Thunderbolt in Soul Silver.
Also, I want to quote Merritt here.
Ho-oh and Lugia do come at a comparable level to the Elite Four, but that's just it: They're comparable. You have a good amount of game to go, but even after all that they're not going to massively outstrip the end game even with (H)G/(S)S's lower level curves. Rayquaza comes at level 70, and you could literally use it for literally nothing besides those Major battles and it'll still curbstomp virtually everything you throw it at. It doesn't take any investment to do this even because Dragon has not resistors in Emerald's remaining battles, so it can get away with never being given a TM. It doesn't even have to fear Glacia much because her Ice types won't get the chance to fire off an Ice move, or if they do the level gap means Ray will probably survive despite his weakness anyway. The most investment it requires is maybe one or two Full Restores and an Elixir.
And take it from experience; Groudon requires leveling to put in work against the Elite Four in Ruby. Natural EQ and Drought Fire Blast are definitely important for Steven's team, but consider that it's a mixed bag vs the others: Glacia is "kill or be killed" for a mon that can be outsped if underleveled, plus Thick Fat and Hail to remove his sun, while Drake's team is all Dragon and 4/5 are off the ground and thus ignore EQ. So Groudon is now asking for level catch up, maybe a TM, to contribute before Steven, and then for Steven he does fine againt most of the team, though Claydol and Cradily can be annoying for bulk and Giga Drain, respectively.
Groudon and the other mascots are A-Rank because they take work and have massive returns. Rayquaza takes no investment beyond actually being caught, it's just a matter of if the amount of game left is enough return for A vs S rank.
I want to close this with my take on why
Rayquaza should be S-Rank. I look at the rankings as a representation of "how likely am I to consider this mon if I want to go for a run that has efficiency as a high if not number One priority". You can debate how much work Rayquaza has time to put in, but when it's grabbed even for some Speed Runs, there's no arguing that an efficient run has every reason to grab him once he's available. Most other mascots earn an A-Rank on the merit of being a very useful team member once available, though being just that: team members, who thus require training with the others and a little healing or thought process. Rayquaza takes a similar stretch of game and literally becomes the "I win" button. You could run a team of 5 Wurmples and Rayquaza through the Elite Four and still have a more than reasonable chance (albeit maybe with a little more item feeding) just because of how his immediate level and power dwarf everything the game has left for the hardest part. The availability vs performance consideration is usually a thing because depending on the rest of your team's levels and types, or willingness to put up with RNG, maybe you don't need the legendary to make your run more efficient (DPPt come to mind for how much work Chimchar and Starly put in from Route 1). I think Rayquaza represents S-Rank because like those two, there's little (or no in this case) question that catching and using him makes the run more efficient once he's been acquired. Even if you got Rayquaza with timing like Zekrom/Reshiram in BW, the fact that the game freely gives you a Pokemon that wins everything that comes after means it is by all means efficient to use it for what comes after, however little or much that is.