It was written to flash by untrusted software, it may have been modified on the way such that it thinks it's unmodified, such that the signatures match when it checks itself, but actual execution uses a modification by that untrusted code.
It's a bit like that paper about modifying the compiler. https://www.win.tue.nl/~aeb/linux/hh/thompson/trust.html
From the owner's point of view, being able to update the ROM is the manufacturer's statement that nothing done by a user with physical access survives.