Encounter Designer
What the encounter designer in the book uses is extremely conservative. I would look at it as if an encounter isn't deadly, it has almost no chance of risking death to a party that has full resources. (barring some oddball ability)
DM Leniency:
Honestly, I think a big chunk of "too easy" stems from DM's refusal to go for killing blows. Which makes unconscious just a damage sponge. A melee attack against unconscious target crits, which is 2 failed death saves. Meaning it only takes 2 attacks, or 1 attack and a failed save, to finish off a character for good.
Further, DM's do not run the NPCs to their full potential, an equal number of goblins can easily be deadly for level one adventurers:
If the goblins are hidden in dark, and the players are approaching in the open and one of the players has a torch, the goblins get a surprise attack at about 80 feet away, all with advantage (darkvision only sees to 60 feet away, but the goblins can see the party due to the torch). Now your party has taken 4 attacks with advantage, if they are to attack back they will be at disadvantage (unseen) and likely against 1/2 or 3/4 cover depending on how the goblins are hiding. If the goblins rolled high, they might get 4 more attacks with advantage. The goblins can continue to retreat and strike, hiding with bonus actions to maintain advantage.
Any caster is also subject to how they are controlled. Do they let their henchmen protect them or do they charge into melee?
Official Campaigns:
Official campaigns do NOT use the suggested encounter guidelines. In Curse of Strahd you can easily run into 3 Night Hags that are in a coven (CR 7) at level 3. If you assume a 5 person party, that is an adjusted difficulty level 8.7 times higher than deadly (the highest difficulty level listed of an encounter). If you run this encounter as the hags would actually act, you will kill the players, probably all of them, but maybe one will escape if they flee opposite directions.
Similarly, some encounters in Storm King's Thunder are reliant on artificially restricting the actions of NPCs so they are not a threat.