The example that you link seems to indicate that you are downloading different files, one link indicates Pan proteome, the other indicates one specific proteome.

The interface could use some work and specificity,

even so, I don't read the above links as indicating that the same data will be provided at both.

Indeed, as suggested by Istvan Albert above, the first link leads to the Pan proteome, i.e. the full set of proteins thought to be expressed by a group of highly related organisms (e.g. multiple strains of Candida auris) (https://www.uniprot.org/proteomes/?query=candida+auris&sort=score) as described in https://www.uniprot.org/help/pan_proteomes .

The first link however leads to the set of proteins encoded by the single proteome described in the page, i.e. the Candida auris reference proteome, strain B8441.