SB Settings and themes are both legal too .
By the nature of code injection, no derivative work is ever created - since extra code is injected directly into RAM. If you own a device, you're perfectly entitled to put whatever 0s and 1s you wish into its RAM (which is all code injection does). That's not creating a derivative work, that's using the hardware you've bought.
The code in RAM is just a protected by copyright as the code on the flash drive. But that is certainly a good argument. I doubt it is as straightforward as you describe because app sandboxes would have to be bypassed and apps would need to gain access to areas of the OS that are unavailable to App Store apps. But that is outside of my area of knowledge.
If jailbreaking in any way was illegal, do you not think Apple would have moved to shut cydia, or its repositories, down (which, let's face it, wouldn't be hard)? Yes, people do illegal things with it, but providing an avenue to do illegal things isn't illegal (i.e. I can illegally import things by driving them through the channel tunnel, but that doesn't make driving through the channel tunnel illegal).
Again, jailbreaking is absolutely legal for specific purposes. Read the exception that you linked to:
"Computer programs that enable wireless telephone handsets to execute software applications, where circumvention is accomplished for the sole purpose of enabling interoperability of such applications, when they have been lawfully obtained, with computer programs on the telephone handset."
And, no, I don't think Apple would move to shut down cydia for much the same reason that they don't move to shut down hackintosh projects.
Also, there is no real "for limited use" clause I found - they made 3 main points:
You are quoting the EFF's opinion. Not the copyright office's decision.