These days it would also help to know the method of publication you plan to target — hardcopy books, digital media
Apple still saves Adobe PDF 1.3. With this version of the document description model, Apple is limited to the standard rendering specification ISO 15930 PDF/X-3 which deals with management of colour information, but not with management of character information (semantic information and structure information). ISO 19005-1:2005 PDF/A is a standard rendering specification based on PDF 1.4 as well for management of colour information as for management of character information (structure information and semantic information).
In other words, the support for management of colour information is there but is truly tough to use and support for management of character information is not there at all.
It is incorrect that QuarkXPress is usable for computerised full character cataloguing with PDF. Quark management mailed the technical press (me and a chief editor) that support for searchable PDF was not intended in version 7.
Adobe had no software whatsoever that supported structure information and semantic information in 2002; that has come trickle by trickle and if e.g. in Adobe InDesign CS (ID39 a searchable PDF is placed in an InDesign page and re-exported, the nested PDF is not searchable.
Henrik