There are people attempting to unravel the template format (why Apple had to change it in Xcode 4 to this weird new system we'll never know) for coding other projects too. You aren't alone in trying to decipher it, but only asking for help via the Arduino on Xcode project means the audience is pretty small. I'm sure someone will figure it out (or it'll get leaked from Apple) sometime.
You're right that Xcode is really designed for OS X and iOS, Apple has little interest in supporting other languages/platforms. Despite its limitations though, I'd personally rather use Xcode. NetBeans is Java, which is usually pretty clunky and un Mac-like. I don't have experience with anything but the Arduino IDE, and Xcode on the Mac however.