> That's exactly what they do though.
> and internalizing this is extremely important for beginning math students.
I'm not saying that you're wrong, because, well, you aren't. But does the choice of notation help here? Understanding that a matrix isn't a linear transformation but only a representation of it is something that's inherently hard and requires a certain level of mathematical maturity. At that point in a sense notation doesn't really matter any longer.
> But undeniably S-expressions are superior from a teaching point of view as they don't hide the "true" structure.
That's exactly what they do though. A group G is not the same as a particular choice of presentation, and an element of g is not a particular tree of generators. Linear transformations aren't matrices, numbers aren't decimal expansions, polygons aren't lines on a chalkboard - and internalizing this is extremely important for beginning math students.