Deoxys-A doesn't belong in the same category as Lati, Kyogre, or Groudon. It's a luxury Pokemon while the others form the offensive and defensive backbones for pretty much every team archetype. Lati is mandatory, and using a Kyogre or Groudon is nigh mandatory. Some of the scariest teams use both.
Yes it is a powerful offensive Pokemon, but it's more comparable to Mewtwo, Snorlax, and Blissey in that it's extremely effective for the style of builds that elect to use it rather than being a foundational Pokemon for the tier. It's basically a faster Mewtwo that has more immediate power and Extreme Speed while having less defensive synergy, no boom, and no Fire Blast.
I feel you also overhype it as an offensive Pokemon and ignore the ways in which teams can prepare for it. CB sets are prone to Pursuit, Protect use, phys def Pokemon, and can't immediately beat the types of Pokemon strong defensive squads employ (Jirachi, Skarmory, Salamence, bulky Groudon). That's not counting the ways offense squads handle CB Deo-A. As for the Sub Petaya set it's also not without its weaknesses. While it is far less vulnerable to Pursuit, Protect use, and phys def Poekmon it can't consistently harass opposing teams as well as the CB set because it has a far lower immediate damage output and relies on having one opportunity to sweep. The set functions best when kept hidden in the dark as the win condition, but this comes at a cost; you have to play the vast majority of the game with only 5 Pokemon as seen
here. The Petaya set also has strong counters (albeit a small list of them) that your team must be attuned to defeat such as Shedinja, bulky Latias, Jirachi, and Swampert. Since it forgoes Extreme Speed it is also easily halted by Rayquaza and weather sweepers.
In short I don't believe Deoxys-A's excellence as an offensive threat is to a degree that is high enough to make it worthy of S Rank. The current S Rank of Lati, Kyogre, and Groudon fit on every archetype, are foundational Pokemon rather than being luxury, have comparable offensive capacity, and also provide immense defensive synergy.
Fireburn also hasn't edited in the prior changes that was agreed on.