There are some who think you should remove the least possible amount of wood from the body for the best tone, but I've also seen it claimed that the large "swimming pool" routing ads a bit of hollow-body-like additional resonance. I remember in the '80s Allan Holdworth had his Charvel Strats routed out under the scratchplate, even though he only used a single bridge humbucker.
I think the truth is that Fender did it to save the costs of having to make different bodies for different pickup configurations, and maybe also to keep the weight down a bit. And now they're basically doing the same with HSH routings.