That you're supposed to agree to. What proportion of the users of Xcode do you suppose have even read that license?
Also the license doesn't prevent you using it, though it possibly prevents you from legally using it for commercial purposes in most developed nations.
With the recent case concerning sending data abroad to process to circumvent patent restrictions it seems that f.lux could just have someone in a country with no copyright/license restrictions download Xcode, compile and make available the software. Apple Computers after all wouldn't own code created with Xcode, which would be a technical rather than artistic work anyhow, so there doesn't appear to be a problem of copyright.
Apple could likely still pull strings that the f.lux people wouldn't find helpful however (maybe the devs have other apps that Apple could block, for example).