The only way to make a campaign world that only exists in the heads of the gamers immersive and believable, is to apply logic and reproducibility even, or especially, to such fantastic elements as magic. As a DM you will get those questions where all the giant fingers come from and you want to be able to answer them. Without achieving a decent level of verisimilitude or some overriding stylistic element that replaces it, campaigns usually don't last long because players stop taking it serious. BG3 takes place within a region and few tendays in Eleint 1492DR, so after the events of the game there aren't so many giants missing fingers, yet. But you correctly identified a huge issue with scale.
You're also right that an ancient dragon would surely wipe the floor with a bunch of dragon hunters, but the youngling black dragons which controlled the troll population in my example were no match for a high-level party. In most RPGs, dragons become more dangerous with age. Pulling out an ancient dragon in a swamp that wouldn't support it only as a punishment to dragon-hunting players, would have been instantly gratifying, but it could have knocked the players off the path of the planned campaign which was about a proper ancient evil in a different bog that had chased those young dragons into their new habitat in the first place. It would also have caused more of those giant finger questions - like, why has nobody ever heard of an ancient wyrm in our backyard before, what did it eat, and why didn't it react to earlier campaign events that would have affected it? Of course, you can come up with conclusive answers, but you'll do those repairs on time you should be spending on pushing the campaign onwards. Also, if the ancient wyrm survives the encounter as intended, what will it do next? You end up derailing the campaign if it attacks the home of the heroes next. Instead, I ended up with players thinking they had achieved victory, only to find out they were wrong, and not only wrong about having won, but also about killing five teenage dragons who were victims themselves. In terms of role-playing, this was way more gratifying!
Those red dragons who serve as Githyanki-steeds aren't always happy about it, but it's a deal struck with their goddess Tiamat and since it's usually younger dragons doing that, it's also a nice way for them to gain experience while doing what they love - carnage and infernos.
