The presumption of innocence is simply that - a presumption
Presumption: the act of believing that something is true without having any proof.
The truth value of the presumption is undefined and not relevant.
It is therefore the starting point of the legal process: the Crown will attempt to provide proof through evidence that the presumption is not true.
This is no different from the null hypothesis in social science, the assumption in a mathematical proof by contradiction, or the starting point of a deductive argument in philosophy.
In any specific instance, a person is either objectively guilty of the alleged crime or they are not guilty. At the end of the legal process, they will be found guilty or not guilty (or, more rarely, neither). In an ideal world, the finding will match the objective reality but, we live in this world.
As a society, we have decided that it is better for the guilty to go free than the innocent get punished. Therefore, in general, we adopt the presumption of innocence and require the state to prove guilt. There are societies where the opposite presumption is made - the accused is presumed guilty and they must prove their innocence. They function as societies perfectly well.