That leaves item A. And it is mostly a matter of determining what is the best mechanism for getting people to know how they should "spell" the metegs with the minimum of confusion. Putting something in the Unicode Standard might be appropriate, or there might be better venues to document the conventions.
I'm of the opinion that conventions that use characters of general category Cf are best documented in the standard. Otherwise, a consistent treatment of such characters across implementations depends too much on context (e.g. use of a particular font).
"Fine typography" issues for other characters, incl. combining are a different matter. These will legitimately differ even among uses of the same character (viz. math and text handling of accents, for example).
A./