The rev-limiter prevents you from over-rev when you are on the throttle. That's built into the ECU to cut power at 8300RPM (this is where the rev-limiter actually is)
However, if you miss a gear (shift from 5th to 2nd for example), that is a mechanical over-rev. The wheels are attached to the transmission that is attached to the engine. The wheels are on the pavement. It is sudden and devastating, and since you are not pressing the gas, the ECU cannot protect you.
Basically, in summary, the rev-limiter is a computer feature. The computer has nothing to do with your inability to shift properly and cannot protect you.