My rule of thumb is that once I start writing imperative LaTeX with loops and stuff, I'm almost always on the wrong path. Now, I might be missing some important corner cases, but by skimming through the blog post, I feel like the author's solution is too complicated. For example, I don't get why this requires auxiliary files.
I would create a counter for the affiliations, let the \affiliation command define macros that contain the name of the affiliation and the value of the counter and then append the output to two different helper macros, one for authors and one for affiliations, whose contents I dump in \maketitle.
I would create a counter for the affiliations, let the \affiliation command define macros that contain the name of the affiliation and the value of the counter and then append the output to two different helper macros, one for authors and one for affiliations, whose contents I dump in \maketitle.