Universal Binary is indeed an Apple branding and certification program. The technical details are but one aspect of it (albeit the most important.) Check out http://developer.apple.com/softwarelicensing/agreements/maclogo.html for an overview. Software developers have to sign a licensing agreement before they can use the Universal Binary logo on their products.
Regarding the fact that both architecture's binaries are contained in the same file: It is correct to express that as "two versions of the program come in the same box" (or more accurately, on the same CD.)
Apple has done a good job leveraging open-source technology for Xcode. It still isn't an accepted international standard, which means you are dependent on Apple (or whoever) for future enhancements. There is nothing wrong with that, if you don't mind putting your coding effort in the hands of other people. That is the trade-off you accept when you opt for a multi-platform development tool.