Now that Apple has officially relaxed that policy, however, Unity's David Helgason is doing the equivalent of a victory dance on the company's official blog, saying that Unity respects Apple for "coming to the right conclusion, and in our eyes it's best to let bygones be bygones!" Yeah, he's kind of excited.
Not that he's admitting the rules were make or break for Unity -- the company was apparently talking to Apple periodically, and even had a workaround ready to go if Apple ever did crack down on the platform. Helgason also points out that, even while things were up in the air, Apple continued to approve and, in some cases, feature lots of different Unity-created apps. While Apple preached against using anything but Xcode to create apps, the app review team allowed and even endorsed the products of third-party development tools.
At any rate, the issue is settled now. Consumers are the real winners here. An end user probably can't tell the difference (if done correctly) between a third-party app and an Xcode app, so the more options for developers, the better.