Sometimes, for a given language, e.g, Persian, there are more than one system for transliteration and the researcher needs to choose one of them. In such cases, shall we tell our audience what system have been used for transliteration? If yes, where is the best section to put it in an academic journal? In the methods?
It is unlikely that you need to specify in your references which system of transliteration was used. The purpose of the references is for the reader to be able to look up the paper, and this should be possible regardless of the system used.
If you do need to to specify the system anyway for some reason I am unaware of, a footnote attached to the reference(s) in question would be a good place.