I don't see the hole being that big. For example Apple's slide-to-unlock patent, no one would be allowed to move that functionality into a dedicated chip but that would never happen anyways.
If Stallman's modification of "implementations using special-purpose hardware" was in place and Apple was filing that application today, I could see how they would reduce the slide-to-unlock to "slide-to-unlock on a multitouch surface".
I don't think that's right. The regular meaning of special-purpose computer is an appliance like a TV or an iPod, it can't do anything that it wasn't designed to do. The opposite is a general-purpose computer which is pretty much anything that can be programmed such as a PC or a smartphone. Of course it would depend on the legal definitions to know what the exact loopholes would be.