Standard diodes as a shunt regulator might be problematic since their forward voltage varies so much between 0.1mA, the minimum current necessary to operate many 431 variants, and 50mA, the transformer's maximum output current rating. Using a 431 provides a much more predictable value.
If you use a TLVH431, a lower voltage 431 variant, you can go down to 1.24V shunt voltage if you want to.
As far as protection is concerned, in my version of the circuit, that is already taken care of by the filter capacitor if you make it large enough. Depending on exactly what you want to measure and the accuracy you want to achieve, this may or not be adequate.