[thaumasiotes]

No, that's not a relevant concern. In the same way, Unicode sees no problem with assigning LATIN CAPITAL LETTER I (U+0049) and LATIN SMALL LETTER I (U+0069) to the glyphs of the Turkish alphabet that have those appearances, despite the fact that in Turkish they are two different letters. (And therefore capitalization has to be done by an algorithm that is aware of what language you want to do capitalization in.)

By contrast, GREEK CAPITAL LETTER A is U+0391, separate from LATIN CAPITAL LETTER A. There is no principled reason for this.