Some of this has to do with the scope of the preference. Layout options apply to a layout; Engraving options apply to the entire project, and Notation options apply to a flow. Time signature design is in Layout Options because you might want big time signatures in a score layout and normal time signatures in part layouts. But there are other time signature options in Engraving Options, and even one in Notation Options.
I agree that this takes a little getting used to, but in the end it’s a very powerful system.
Here’s also a post from Daniel laying out some of the thinking behind this.