They are artificial creations. Like our current tech, they are designed using modular components, and they accept updates in the field. My Blu-Ray player or dishwasher downloads new firmware; Industrial enginines by IH can have features like total horsepower unlocked or configured by software while in-place.
So consider the “upgrade” to be designed as something like an in-app purchase from the original maker.
With the loss of original maker and the (actual) evolution of the forms as they became feral, the code is a bit mixed up, like with the Dragon’s Teeth of Mirabile by master world builder Janet Kagen. Rather than buy an unlock code, the needed triggers are found by side-effects or evolved access to useful survival traits by the feral form. You might read Kagen's stories to bet a feel for what I have in mind about the DNA.
Being modular, distinct traits like limbs can be recessive or switched off or damaged in a feral remixed offspring. Many features are simple configuration options using common code. Although inspired by legacy bioforms that were unrelated and incompatible, the engineered lifeforms used inter-compatible standardized traits and developmental configuration programming.
Now in ourselves such a change like extra toes would only be effective in the germ line, as development occurs once. But these animals were designed for having upgrades applied. Re-development — metamorphosis — was designed in so changes could be applied to existing pnenotypesphenotypes.