That's a very good question, and the answer is probably "Plot Armor."
BUT... If we want to come up with an in-game justification,
it is Orpheus' power that keeps everyone from transforming. Presumably, even as a mindflayer he should have that the power. Likewise, if someone else becomes the mindflayer they eat his brain, keeping the power active.
Additionally, the PC/Orpheus/Karlach mindflayers look different than either grown mindflayers or the newborns we see elsewhere. So... is it the same kind of mindflayer or has the Orpheus protection of the magic used by the Absolute to suspend them affected the transformation? Even Omeluum asks if his race is evolving.
In reality the appearance difference has more to do with rigging to incorporate the animation of the figure in the end dialogue, but hey, we can still use it for head canon.