A disappointing moment
Answers
Yes, the DPS/TDO rankings are for level 40 pokemon.
What you said is absolutely correct if we're talking about powering things up specifically for soloing the Flareon, but the Rayquaza was more likely used because it happened to already be powered up. Ray and Mewtwo can help in a lot of different teams because their neutral damage is so high. I'd rather pull through with something I can cobble together on the spot instead of having to power up more counters for a specific raid.
I would totally agree with the approach if we were not speaking about Kyogre. This legendary is more useful for solo raids, at least looking at our raid history. It is a "supreme" counter (not a "good option") for current Flareon and Donphan, and then legacy Onix, Aerodactyl, Claydol, Ninetales, Arcanine, Lunatone/Solrock, Piloswine and... well, duo Shuckle. I don't think there has ever been a more useful Pokémon for Tier 3 solos than Kyogre.
I just did now a "Fire Blast" Flareon solo with "Partly Cloudy" weather- team composition:
L40 14A SD/SE Tyranitar*
L38.5 15A SD/SE Tyranitar
L34 15A Wf/HP Kyogre*
The rest (worse 2x Kyogre and 100% L40 Gyarados) were not used, 2x FB dodges with 1st Tyranitar, 1x with 2nd one, the rest I just tanked, 34s on the clock. Without weather boost, it would be pretty much borderline or fail, but I wouldn't have dodged at all either, so it's hard to tell...