That is not exactly true. They wrote the OS, they designed the phone, they know where the JTAG connectors are. Cracking the phone apart and putting is logic board up on a debugger would likely enable them to bypass security.
From what I understand Tim is doing, and I greatly admire, is trying to avoid a judicial requirement that they be able to do this on demand. The so called "back door" requirement, because he knows, as others do, that such a feature would be used by more than the intended audience, and for more than the intended uses, to the detriment of Apple's users.
What I really find amazing is that I was at a talk hosted by the East-West Institute where the Air Force General of the new cyber command (whose name escapes me) complained that "we" (silicon valley) had let the government down by not writing strong enough crypto to keep our adversaries out. I remarked that it was the ITARS regulation and the Commerce department at the behest of the NSA which had tied our hands in that regard, and that with a free reign we would have, and could do, much better. Whit Diffie was there and also made the same point with them. And now, here we are 10 years later, and we "fixed" it, and now its our fault that they can't break into this stuff? Guess what? Our adversaries can't either!
The right to privacy, and the right of companies to secure that right with technology for their customers, is a very important topic and deserves the attention. I am really glad that one of the most valuable companies in the world is drawing a bright line in the sand. So I really support Tim's position on this one.