Your last paragraph isn't saying anything. From my perspective, all of that would be true. And it would be consistent. From the CT's perspective as well as the actual Verse in the last paragraph you say would be Canon. Why is it inconsistent, really? Because I think the idea that there's no limits to TRAINED Pokemon (as this would only apply to important trainers who actually fight against the protagonists, if at all, considering most of the time the protagonists are effortlessly defeating everyone and everything.) actually fits in with everything.
You keep saying that it's obvious that it's inconsistent, and that the whole verse can't be 2-B-- with no real evidence or argument that's not a fallacy. So what if everyone who scales to the legend wielding protagonist trainer is Legendary Tier-- if they even scale at all! Hell, I think that they might not really scale because we could write any battles where the protagonist one and canonically had a Legend on the team as a STOMP! They don't even have to really scale, but I'm arguing to point out how this logic we're using doesn't make sense.
You showing me that everyone would be Legend Tier isn't an argument-- you're literally trying to appeal to the idea that X claim must be false because X means that Y is true, and Y is ridiculous. This thought process only works if Y cannot be true at all, when the games show that it is. As for the Master Ball shenanigans, I think THOSE are the real PIS. When you really check the Anime, when (besides that one time in the beginning with Ash and Pidgey, and that Pidgey still broke out of its ball by the way) has a basic pokémon ever gotten captured against it's will? There probably were some instances, but those were already inconsistent within the lore anyway, as in other places, we see Pokémon get hit with Pokéballs and get caught, whereas in other places, Pokémon knock back pokéballs with PHYSICAL CONTACT all the time, regardless of their level or the pokéball used. So to say that is an example of how Pokéballs are fodder isn't necessarily a good argument when in THOSE mediums specifically, the process of obtaining a Pokémon is already filled with weird shit anyway.
It's weird shit, because that means that no pokémon should ever be caught in a Pokéball ever because they can just knock it away. Like, no, by your logic, Pokéballs can't catch ANYTHING, including fodder!
TL
R; Just because everyone in their mother becomes 2-B doesn't make my argument invalid. You're trying to make an appeal to emotion by pointing out how absurd it sounds, which is an argument of incredulity as well, and a FALLACY! The only way that works is if it's IMPOSSIBLE for trainers to fight, weaken, capture, or even remotely harm CT in any way-- and it is only TRAINED PKMN that could get the scaling IF ANY in the first place. And we know that in the game's it isn't true that it's impossible to harm a legend, and every other instance of it happening in the CT's case is CONVENIENTLY (or correctly?) PIS when it comes to the anime. It's not based in any fact, your argument.