Which one is harder? Which one is more scary?. I think the main game is easier, the first time i played I can actually predict when and where the monsters will spawn. But in some custom stories ( is made by many different people), made it harder to predict.
There's huge variability. Some custom stories are incredibly well done, others fail to really hit or set a benchmark. At the end of the day, the game and any creations shouldn't really be compared by difficulty or script prediction - rather the content, how it is revealed to the player, the differences and the aspects which make it playable and how it is remembered.
A:TDD ticks every box in it's originality, differences in comparison to Custom Stories, and spectacular use of it's own script. Most custom stories fail to really stretch the capability of HPL2, and while they don't necessarily need to, they do need to make you feel like your not just playing another one of those Custom Stories, but an entirely new one worth playing.
Well the thing is that while the main game is, well, one predictable (after the first playthrough) story, the Custom Stories are all unique and one is not like the other so some Custom Stories are easier, some are harder.
As Romulator said, it's a huge variability when it comes to Custom Stories.