The server-side PCS logic (mobile-html) performs a lot of very complex rearranging of Reference elements in order to accomplish a specific presentation style, which is only slightly different from the style of mobile web.
This current logic is tightly coupled to the structure of the base Parsoid output, as it existed at the time PCS was built. However, Parsoid itself has evolved since then, and also the Cite extension is planning updates (i.e. subreferencing) that will be wholly incompatible with this logic.
Ideally, any unnecessary DOM manipulation of references should be removed, and any styling should be done with CSS.