Greek numbers in Unicode

Question: which of the various Unicode codepoints for Greek numerals (in the U+03D8-U+03E1 range) should be used by preference?
Speaking descriptively not prescriptively:

(1) Re the upper- and lowercase forms for archaic numerals, although of course all characters on inscriptions (and presumably seals) are technically uppercase, editors may choose to render then in upper- or lowercase depending on editorial preference, and in some cases this difference is even meaningful (lowercase representing units, uppercase thousands, for example). Unicode merely reflects this practice. While we would probably strongly recommend anybody using these to be consistent within their project/corpus, it is surely possible to impose consistency across the field.

(2) Re the two qoppas, Q-form (Ϙ,ϙ) and lightningbolt-form (Ϟ,ϟ), the Q-form is the archaic letter and was used as the numeral 90 throughout antiquity. At some point (in the print-era) the lightningbolt-form, which is a mediaeval orthographic development of ϙ, replaced the numeral and is now so used in modern Greek chapter numbers and the like. The two are unlikely to appear in the same text with different meanings (unless potentially a modern Greek edition of an epigraphic corpus, but the contexts would also be very clear), but Unicode has clearly decided to encode the two as separate codepoints. I would suggest that when encoding ancient Greek texts, we always use the Q-form, whatever the actual shape of the glyph on the stone/seal/page. See Wikipedia on the history and use of the letter qoppa.

(3) The situation with the "stigma" (ϛ) and F-shaped (Ϝ, ϝ) digamma, when used as numerals, is similar but not identical to the above. The latter is also sometimes an alphabetic character in archaic or dialect Greek, especially inscriptions, Sappho, etc. Encoding numerical ancient digamma (6) using the stigma codepoint is more common, however. See also Wikipedia discussion of digamma.

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(see also Greek Fonts (variant character forms))