Please see https://fa.wikipedia.org/wiki/User:Huji/T266415
In Scenario One everything works as expected. In Scenario Two, however, we expect the second ref to be shown in RTL in the references section, but it is shown in LTR.
In an initial analysis of the DOM, it seems like the "mw-cite-dir-ltr" class definition from modules/ext.cite.style.fa.css never reaches the browser.