From what I can tell, it has to do with the indexing that is done on the PDFs to make them quickly searchable.
When I open a Paizo PDF in Preview in the native 64 bit, it maxes out both cores of my CPU, but Preview is only about 60% of that. the other 40% or so is 'mdworker', which is Mac OS X's indexing process. I'm not sure why it works OK in 32 bit mode, but it does.
Also, a quick tip: I created a copy of Preview.app and renamed it Preview32.app. I changed the setting on that one to open in 32 bit. That way I can have the native 64 bit version handy without having to change the settings back and forth.