The DMG custom monster rules are very exploitable. It's trivial to create a CR 1/4 creature that can kill Frost Giants with ease. Here are some things that are "free" for a CR 1/4 monster:
Arbitrarily high movement
Teleportation
Ranged attacks as long as they don't deal more than 8 damage on average
An arbitrarily high number of Legendary Resistances
Immunities to an arbitrary number of conditions (exhausted/charmed/stunned/etc.)
Immunity to fire/cold/force/blunt/piercing/slashing/magical weapons/etc., as long as you halve HP to compensate
Arbitrarily high ability scores, as long as they don't increase damage dealt or total HP (INT 24, WIS 24, CHA 24, CON 24 as long as you give it a small base HD)
I forget whether you can get spell immunity for free as well, but 50 Legendary Resistances is pretty sweet already.
In short, the DMG rules are okay-ish as a formula for telling you how much experience a given creature is worth, since you gotta have something, but they're quite bad at telling you how genuinely dangerous a creature with special abilities is. If you create a custom monster, and it isn't just a sack of HP with a melee attack--suppose that it has a ranged Entangling attack and can teleport as a bonus action to snatch entangled prey--it's guaranteed that the DMG guidelines will underestimate its lethality.
On the plus side, the DMG encounter balancing guidelines already underestimate PCs' (potential) lethality, so tricksy monsters against tricksy PCs might actually be a fair match.
As an aside: one of the best advantages a monster can have is looking so much like a weaker monster that it gets underestimated. In my world, PCs benefit from this constantly. They look just like regular, weak old humans. A squad of 12 hobgoblins doesn't run away from three PCs when they see them coming because the hobgoblins assume they will win! If hobgoblins have been warned by the survivor of a previous battle, or if the PC Necromancer raises an army of skeletons, this ceases to be true, and the hobgoblin squad takes the threat as seriously as an enemy platoon (break contact, skirmish at range while waiting for reinforcements to arrive in force--all the things that frustrate PCs).
I've ran about 40 custom monsters now, and if you avoid obvious exploits and stick with the spirit of how monsters are created, it creates exceptionally good monsters that feel challenging at high levels.
My experience simply does not match your theory. I think if anything you over estimate the lethality of certain abilities. Combat simply doesn't last long enough and you generally don't stack a ton of riders on one monster.
Let me tell you players fear "bags of hitpoints" when those bags of hitpoints can do enough damage to kill them in one turn.
Believe me, when I first read the DMG rules, I hated them. I thought they were hard work, inaccurate, and missing so many factors. But after actually using them a lot I have found the underlining assumptions are correct. It really does just come down to how much damage and how quickly you can put it out, and how much damage you can withstand.
Honestly unless you have an action economy advantage a lot of effects are not worth the cost of the action. A creature can teleport around willy nilly but it's not really doing damage while it's doing that, and in three rounds it will be dead. Better just to hit and hit hard.
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