[strikethrough] That has not been my experience, although I admit I haven't jailbroken an iPhone in quite a while. But this used to be how PwnageTool worked - it unzips a stock iOS image, modifies it, packages it back up, and lets you install it on your phone through iTunes.
I'm absolutely certain that this is something Apple can detect and could have prevented if they wanted to. [/strikethrough]
Also, e-fuses and trusted computing thingamajigs can be used to constantly keep the integrity of the core OS components (bootloader, kernel, launchd, etc.) in check and either brick the device or, more likely, to refuse to boot or continue running the OS until it has been restored. So, no, I disagree that Apple are using all the effective technical measures available to them. Apple are using all the measures that they think is worth investing resources in, given the magnitude of the problem (which seems to be right now tiny to nonexistent).