Ahnehnois, would you cite your source? I would be very surprised to hear that the authors deliberately broke the CR scores in order to trick DMs & players into overly-difficult encounters. I would like to read about that from those that said it.
For my part, I suspect the authors just didn't get the CRs right. I'd alter every single CR listed for every single dragon to be at least 1 CR higher. This assumes that you are a DM who understands how to run a dragon encounter well. This also assumes that you do not cheat, do not break rules, and do not deliberately railroad an encounter to be harder than usual by DM fiat. Dragons are legitimately hard, so there is no reason to manipulate them.
Regarding the OP, here is my take. Consider Ozyrrandion. He's the first dragon encountered in the module Red Hand of Doom. He's a young green dragon, CR 5. He has 104 hit points, AC 23, flight with flyby attack & hover, a breath weapon, blindsense, and if he can full attack he gets 5 rolls: bite/claw/claw/wing/wing.
Compare that to a hill giant. 102 HP, 20 AC, can't fly and doesn't even have spring attack (so he can't pull off the "hit 'em and get out of range before they retaliate" thing), cleave, rock throwing (ex), and if he can full attack he gets only 2 attacks (but they pack a punch).
You might say, "uh, hey, those are actually pretty similar, so why are you trying to make it sound like the dragon is so tough?" Well, okay, maybe the hill giant is equal to or only a little bit weaker than the dragon, but consider this:
Young dragon: CR 5.
Hill giant: CR 7.
Yeah? The hill giant is weaker or equal at best when we look at the stat block, but he's given a CR that indicates he's 2 points tougher than the dragon. That makes little sense.
When you consider that our CR 5 dragon also gets triple the amount of treasure that the hill giant gets, and that dragons are typically played as intelligent enough to use their treasure in combat, the difference becomes even more dangerous. In fact, we can see that with our example of Ozyrrandion. He's wearing an amulet of health +2, and bracers of armor +3... and the module notes that if he gets hurt too badly, he will pull back long enough to drink some potions and come back into combat buffed.
He is absolutely scary for a CR 5.
When I got to play through that encounter, never having read the module, our adventuring group got badly, badly hurt. And we were level 7 or 8 at the time! Our problems? Where to start? The only character in our group that could fly was my cleric with the travel domain. So you can already guess how ineffective the rest of the group felt, grounded, plinking away with arrows. And with the dragon doing flyby breath attacks, our fighter just stood around with a readied action to "swing my sword when the dragon gets within reach" that never triggered. Eventually the fighter gave up on it and started climbing to the top of a tower in a futile attempt to leap off the tower and at least get one mid-air swing while falling.
Even my cleric with flight had trouble. I couldn't keep up with the dragon's flight speed. At one point I used Dimension Door just to get ahead of his flight pattern.
The player running our sorcerer didn't know much about dragons and so when she managed to blind it, of course she was sad to learn that the dragon had blindsense. Eventually she stood on the ground, hurling fireballs over & over again.
We won, nobody from our group died. So it wasn't a TPK or anything. But compared to almost any other CR 5, man, that was hard.
Dragons continue to outclass the PCs as you go up in CR. The dragons with very high CRs have spellcasting levels, DR, SR, extra attacks & abilities, etc. And the flavor text for dragons indicates that unlike a hill giant who might stupidly stand toe-to-toe in melee, trading blows, a dragon has no interest in that. Fighter climbs to the top of a tower and shouts challenges at the dragon? So? A DM might envision the dragon screaming through the air, landing on the crenelations, and engaging in a brutal combat with the mighty warrior. But that's not how D&D dragons are described. A green dragon will hear the fighter's taunts, get just close enough to spit acid from out of reach, and then fly back even further. It has zero willingness to engage in a fair fight. It makes them even more difficult.
Whew.