I think you're onto something here. It's logical to say that the Fire Sanctuary and the Fire Temple are two distinct lcoations that serve different purposes to two different species, the Fire Sanctuary is the place of worship for Eldin, but the Fire Temple is perhaps devoted to the worship of Din by the Gorons who would no doubt consider her their patron goddess as they value strength above all else as evidenced in TP.
What is esepcially curious to me however is the location of a Temple of Time in Lanayru Desert in SS, but we see no such place in OoT in the Gerudo Desert so perhaps the Lanayru Desert and Gerudo Desert are in fact, distinct locations but we cannot be entirely certain of this as undoubtedly the Faron Woods in SS and TP would have remain unchanged, and it's possible the Earth Sanctuary and the Forest Temple are one and the same as there is a body of water inside the Forest Temple, but based on its architecture, it was theorized by fans that it would have been a former Hyrule Castle, or perhaps even a former Temple of Time.
Now, I forgot to mention this earlier but I also do agree with your speculation/opinion that such terms as Death Mountain are not insomuch landmark distinctions but placeholders, it's perhaps a name given to any mountain range that was formerly an active volcano, but based on TP's Death Mountain, it was undoubtedly an active volcano, and the geography of the Goron Mines means that it couldn't be a former Fire Temple but a new mining location ala Dogondo Cavern in OoT which likely served as a mining location for OoT's Gorons.
Of course, this does make things very annoying as we can't find a definitive focal point in Hylian geography to base any such consistency or stability, why, it's even theoretically likely that the Lost Woods shift around due to their ambiguous and supernatural premise, and could even morph around to change structures from within. Now we'd think that such locations as Castle Town, Hyrule Castle, Kakariko Village, Lake Hylia, Death Mountain, and Zora's Domain would remain geographically stable, but that's clearly not been true from OoT to TP.
Very confusing indeed.