While I use an alternate challenge rating calculator, I find that for the most part encounters are about as difficult as I expect them to be. There are a handful of monsters, most of which are in the MM, that I either beef up or are extra careful with, but once you account for that and the overall capabilities of the group it's in the ballpark.
You do have to take into consideration the PC group, the environment the encounter is going to take place in, the number of PCs vs the number of monsters, the goal of the group and so on. It will always be more art than science, there is no way to come up with a one-size-fits-all it has to be adjusted by group. I've run multiple groups simultaneously with the same levels, one group could simply handle far more of a challenge than the other.
But that's really encounter design. CR? The foundation? Works well enough for me as a ballpark guesstimate.