If I say something is the "treatment of choice" or the "pencil of choice", etc., does that imply that this is the best of all the possible choices available -- that those who know best would choose this -- or just that there are many choices available, and this is the one that happens to have been chosen at the moment?
In medicine, the "treatment of choice" is the treatment one chooses based upon a set of criteria determined by a particular patient. For example, trimethoprim-sulfamethoxazole is recommended to the prevention of pneumocystis in patients with HIV disease in patients with a CD4 count <200/µL, but the "treatment of choice" for a patient who is allergic to trimethoprim-sulfamethoxazole might be dapsone plus pyrimethamine plus leucovorin. In the example above, trimethoprim-sulfamethoxazole might be described as the "gold standard," the current and most effective treatment, the one against which dapsone plus pyrimethamine plus leucovorin would have been evaluated. (Disclaimer: Don't try this at home except under the direct supervision of . . . .)
I would actually argue that in the construction, "the X of choice," of choice tends to connote either the most frequently selected option or the best available option, rather than the best option overall.
For instance, one could write
For most users, Microsoft Word is the word processor of choice.
That does not mean that Microsoft Word is the best option; it is just the preferred option of those users.
I would draw a distinction between the pencil of choice, which is the best, and a pencil of choice - one of the best. From that point of view, the answer to your title is "merely an option" but to the question (which uses "the..." for both examples) -- "the best". The construction "a [noun] of choice" is less common than "the [noun] of choice".