I agree, and I think this reeks of the Monad Burrito Tutorial Fallacy[1]. Once you know what the manipulations
are you can start to visualize doing them in these weird 3d ways, but the understanding came through the struggle to
make a coherent picture and not the resulting coherent picture itself. The claim that "matrix multiplication is fundamentally a three-dimensional operation" is ultimately very confusing because it conflates the row & column
dimensions of the matrix with the
dimensions of the underlying vector space.
Colorized Math Equations[2] has the same problem where people see it and go "Colors! English language! This must be so much more easy to grasp than math! I feel enlightened for having seen this!" But feeling enlightened is very different from being enlightened and it just doesn't hold up. I've found people retain very little understanding if they aren't already familiar with the concept.
[1]: https://byorgey.wordpress.com/2009/01/12/abstraction-intuiti...
[2]: https://betterexplained.com/articles/colorized-math-equation...
EDIT: The "three-dimensional operation" perspective no doubt comes from writing matrices as rectangles, but this is far from the only representation of them. If the vector v = [a, b, c] is shorthand for v = a x_hat + b y_hat + c z_hat (explicitly a sum of basis vectors), then we can write a matrix with a similar set of basis vectors: m = [[a, b, c], [d, e, f], ...] = a x_hat x_hat + b x_hat y_hat + c x_hat z_hat + ... . There's nothing "rectangular" about this any more than a polynomial (as a sum of monomials) is "rectangular". The details then shake out of how (x_hat y_hat) multiplies with (y_hat z_hat). The rectangle is just a mnemonic.
DOUBLE EDIT: In the above sense, multiplying two matrices is more like a convolution -- the x_hat x_hat term of the first matrix multiplies every term of the second, we just know most of those terms will be zero (the product with any term that doesn't start with an x_hat (e.g. y_hat z_hat).