Because the point of this legislation is to try to do some harm reduction around waves of opiate deaths. It's not about liberalization for the sake of principles, but for a specific public health purpose.
In any case magic mushrooms use and trafficking is already mostly ignored by police is my understanding. I've heard there are shops operating in the open in B.C. The mushrooms themselves grow all over the place there, too.
That is certainly the primary goal of the legislation but reasonable secondary goals might be to reduce uncertainty like you’ve mentioned, and also remove scenarios where the punishment doesn’t fit the “crime”. I just don’t see the cost to have included psilocybin but I see the benefit to including it along with these other drugs.
Now you can have 2.5g if meth and show it to an officer with impunity, but the same amount of psilocybin, an objectively less harmful “drug”, could lead to imprisonment. It’s madness.
Also, it keeps the handbrake engaged on advancement of research and development in new psilocybin based therapies.