I tried to read through all 6 pages, but forgive me if this has been said and I missed it.
It looks like the rust is confined to the fasteners. My guess would be it was either 1) a bad batch or 2) during the assembly process the coating (zinc or similar) that prevents rust was scratched enough to be removed.
Shame on StopTech for not dropping a set of rebuild hardware in the mail with a few stickers and saying they were sorry. However, I don't see this rust as being a ding on their quality (bad lots of fasteners happen) but it is a knock of their customer service. Hopefully they will make (or have made) it right with the OP.
If there are finish issues on the calipers themselves that's a bit more of an issue, but perhaps it's because they figure they are built for race applications where the users aren't going to care? Not that it's a good excuse, but perhaps it's at least a reason?
Anyway, hopefully StopTech makes this right. Good luck, OP.