Do you believe the GPL in all its variations is enforceable? That is, if someone downloads a bunch of GPL's software, should they be bound by the GPL? If a person downloads GPL software onto their own hardware, do they 'own' it? Can they do whatever they want regardless of the GPL?
The GPL functions because software (aka 'intellectual property'. Sigh.) is *licensed*, not sold. There is no transfer of ownership. The owner of the iPhone owns the hardware, not the software. The software is licensed. The owner has no inherent rights to the software. The owner only has the rights granted by the license and under the terms of the license (see the GPL.)
So, the owner of the phone can do whatever they want with the hardware. They can put whatever they want on the hardware... unless they are using iOS, or the Apple firmware, or other Apple software to do so. Apple software is always Apple's and only licensed to the owner to use under the terms of the license agreement (again, this is why the GPL is enforceable. The owner of the 'intellectual property' gets to set the terms of use.) Apple can't enforce what software is run on the hardware, but they can enforce what software is run on their software. (See GPL3 and variants where just 'linking' with other software can trigger the terms.)
The linkage of hardware (which is bought and sold with transfer of ownership) with software (which is licensed) is getting to be a bit of a problem because companies are using the latter to control the former, but this is how the current 'intellectual property' system is set up. There is certain arguments to be made that it should be changed -- but people should probably be wary of doing so. If limits are placed on what the creators of software can and cannot limit in the licenses... there are no doubt many, many companies that would enjoy being able to blow off the GPL class of licenses if such terms were no longer enforceable.
That's the long winded way of saying, basically, yes, Apple does have the 'right' to determine what software iOS on the phone can run. That's what 'copyright' grants them. The right ends at the hardware, but as long as the hardware requires the firmware/drivers/software to operate, from the practical point of view, it's pretty much the same. To say otherwise implies that the GPL on any hardware driver would be invalid. If people claim that Apple cannot specify the terms of use for an operating system, then people will argue that the GPL cannot be applied to Linux.
This isn't a great situation. However, it's not clear how to deal with 'intellectual property' (ugh) in a way that reduces the power of large companies without imperiling smaller companies. I suspect because of this most of the cases will fizzle out because the judges will want to punt the issue to congress (particularly given issues of international commerce/copyright treaties) rather than make dramatic rulings.