Apple won't allow you to run youtube-dl on your iOS device. Section 2.5.2 is just the excuse. If 2.5.2 didn't cover it, they'd make up another rule to do so.
Apple isn't going to let people sidestep copyright on iOS. It doesn't matter whether youtube-dl or curl or wget have legitimate uses. If they can be used to sidestep copyright, Apple will ban them.
I'm an Apple user. This pisses me off too.