Well, Apple didn't treat Flux any differently than other developers who used private APIs or tried to distribute binary blobs to iOS users.

Software running in the background is something Apple tightly controls in iOS (battery life and security being major concerns). They also don't let apps make changes to the OS appearance. That may be the wrong approach, but Apple is at least consistent in it. This was either an OS level feature or a no go from Apple's perspective. As a user I'm happy it's a feature!