Sciencemaster:..."Is there anything else I'm missing here?" I would say you are missing the basic property of a linear transformation, namely it is entirely determined by its effect on a basis. For the same reason, a linear transformation only has one matrix in the standard basis. done.
I.e.
1) The eigenvectors and the eigenvalues completely determine the linear transformation, assuming the eigenvectors contain a basis.
2) A linear transformation completely determines its (standard) matrix.
These are both for the same reason, namely that a Linear transformation is determined by (and determines) its action on a basis. Thus if the eigenvectors contain a basis, knowing them and the eigenvalues tells you what the transformation does to that eigenbasis, hence determines the transformation on everything. Now that we know the linear transformation, we also know what it does to the standard basis, which uniquely determines the (columns of the) matrix.
It has absolutely nothing to do with the existence of a diagonal matrix.
I.e. if you know the behavior of any linear map on any basis, then that map has only one standard matrix.
I apologize if this is still confusing. It confused me too. I at first thought I should use the diagonal matrix somehow.