I think you are rigth. Our dissagrement comes from thinking the metaphor refers to structure rather than just language. Lets say an atomic model were the electrons ar flying around a nucleus formimg shells, is also not literaly aplicable. But we think of it as a useful metaphore because its close enough.

The same should apply to the most sophisticated mathematical models. A useful metaphor should then be a more primitive form of thise process where it illustrates a mechanism. If the mechanism is different from the mechanism in the metaphor then it should be wrong.

If the metaphor is just there to provide names, then you are offcourse rigth that it should not change anything.

Whether the metaphor of computers and brains is correct or not should also have no effect on wether we can simulate a brain in a computer. Computers can after all simulate many things that do not work like computers.