I'm with mayoor. To my understanding, PDFx1a (v1.3) is basically a "lowest common denominator" approach that most printers should be able to handle. And in the PostScript and distill method, the act of PostScripting in itself does the flattening, so it doesn't really matter what PDF version you distill to, it's never going to be any better than a PDFx1a.
What inkspot may not be doing, and he can correct me if I'm wrong, is checking the transparency flattening before exporting to PDF to eliminate possible problems. I'm not going to go into details because Michael Murphy has a good video on the subject: http://www.theindesigner.com/p…..ner_23.mp4
The video is from 2006, but the Flattener Preview really hasn't changed much through the versions.