It's admittedly confusing that you configure this at both the course level and the assignment level. Originally the thinking was that you need to be able to enable/disable it at the course level because if you are not using it at all, then all the date settings for reduced scoring are just clutter. And then you can enable/disable it on individual sets since it's reasonable that even if you use this feature, you might not use it on all sets.
However I do note that you can effectively not use it on a set by having the reduced scoring date match the close date. So it's at least worth considering that in a future version of WeBWorK, maybe (maybe) we could remove the assignment-level switch here.