Well, yes and no. It's true that notation is a tool and not the actual object of interest (except when it's both), but some tools are much, much better for certain tasks than others.
Imagine, for instance, trying to teach someone about databases and having them demand that you translate everything into x86 assembly first, since that's what they're comfortable with. Once you get past the basics, this is the level of mismatch we're talking about.