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I'm guessing it's the opposite -- to make the "mundane invisibility" hard coded to be weaker than the magical kind. But don't mind the pessimist, folks!
What I was trying to say was that if the benefit of hiding is weaker (you're not "invisible," only "hidden") then hiding itself can be stronger. For example, a magic item that lets you hide at will can be 50% cheaper because it doesn't also give you total concealment's 50% miss chance.