The only strange thing is that you think that you have an argument without being able to point to a single example of this "strangeness". Vague general impressions are a poor basis for an argument - especially when they seem to lack any basis in fact.
Looking at the links it seems to me that the Bristlecone Pine was originally classified as one species Pinus aristata. At some point after the writing of the Science article (in 1968) it was recognised the the population previously denoted var. longaeva was a distinct species. The "synonym" in the Forestry Service article refers to the older nomenclature - while the article proper recognises it as a separate species.