In the physical example, according to the FBI's "just this one iPhone" claim, one would reasonably expect that the company could then destroy the hypothetical master key as soon as it's used. This makes sense in a physical world, but the analogy breaks down completely in a digital world. [Returning your spider doesn't solve the problem](http://www.27bslash6.com/overdue.html).
In the digital world, you can't guarantee that the key hasn't been copied, and you can't guarantee that destroying the "original instance" of the key destroys all others.
The custom OS that the FBI is asking Apple to build will also take development time, and likely take more than one person to develop, meaning that if there's a security breach during the OS's development, any number of intermediate builds may also be stolen during development, before the FBI can even access the particular phone in question.