About the two scientific names: (this answer the botanical nomenclature part of the question, not the cultivar nomenclature, which has a related code and so rules)
Juniperus scopulorum and J. virginiana are not synonymous (not on the usual two meanings). Just J. scopulorum can be seen (by some people) as a
subspecies/variety of J. virginiana, so as Juniperus virginiana var. montana (Ir other variety/subspecies names)
Source: The Plant List: http://www.theplantlist.org/tpl1.1/record/kew-2331595 and http://www.theplantlist.org/tpl1.1/record/kew-2331680 . The plant list is an consensus list of plant names. Note in this case there is not strong consensus.
There are various level of synonymy in botanic:
the first (and usually neglected) is the corrigible errors (usually spelling or incorrect/inconsistent declination/gender on one of the names). (sylvestris/silvtris is one of the common error, also because the correct name depend on the read genre)
homotypic synonym (nomenclatural synonym). (sometime written as triple bar: ≡): different name of the same plant. Just moved in an other genre or in a different rank (variety to species, etc.). When the author changes the name, she write also the original one (with some explanation why the new classification is better), so usually there is no confusion, and both names remain valid (just one will be probably be the "accepted name" of the community).
heterotypic synonym (taxonomic synonym). The type (species, subspecies, veriety) were described as a new one, possibly with a herbarium reference. These are the difficult ones. In the other two cases, there is no challenge possible on synonym, just one can/cannot agree on the new term. In this case, nobody is really sure that the specimen is really about the same species. Maybe in future it will found that it is really a new variety, of just a special form because of environment.
For completeness, there are also autonym: e.g. the original Juniperus virginiana will have automatically a name Juniperus virginiana subsp. virginiana when an other subspecies is named. Older high ranks (families, divisions, etc.) receive automatically a correct suffix.