Neither. I'd expect Apple to do what they usually do—grant exceptions on a case-by-case basis for developers who have specific reasons to need to do those things.
So here's the thing. I understand that f.lux has patents on their way through the patent system. Chances are, Apple is infringing them. My advice would be to try to work with the f.lux people now to get their product in the App Store and keep them happy.
It sounds like a token amount of effort (an API usage exemption—probably little more than a custom provisioning profile) would satisfy them and keep this out of court. If that's the case, then Apple's management would have to be utterly stupid to not do so.
The longer they are blocked from selling their app while Apple uses potentially infringing copies of their technology as part of the OS, the bigger the potential damages if this ends up going to court later, and the more likely they are to be awarded treble damages for willful infringement.
And even if it later comes to light that any patents f.lux holds would not be infringed by Apple's implementation, they still haven't lost anything, and they've gained a fair amount of good will with the developer community.