Courses that fall under the LOTE category are generally taught to an audience to whom the target language would be a second/foreign language. In fact, this does not only apply to Stage 6 subjects, but also to language courses taken by non-school students. Because of this, the standard version of the language taught would be used, especially for Beginners, Continuers and Extension courses. This is the case of languages such as French, where the standard/metropolitan/Parisian French is covered (instead of Québécois French for instance). The syllabus documents of both Spanish Beginners and Spanish Continuers state that the language to be studied and assessed is modern standard Spanish (what I believe is also referred to as Castilian in Spain). Based on this, it is most likely that elements that constitute other variants of the Spanish language will not be emphasised in the Spanish course(s) that you wish to take (from your post it seems that this would be Spanish Continuers with/without Spanish Extension).
With that being said, it is reasonable to expect that you will explore the Spanish-speaking world at some point during your studies (including themes such as multiculturalism). However, it is unlikely that this will extend to cover differences between standard Spanish and other variants of the Spanish language.
I hope this helps!