The reason we have characters like ` and ~ in ASCII is because the designers were targeting teletype machines, where you could type accented characters by overstriking punctuation onto lowercase ones. So I figure that's a good enough way to handle them without increasing the size of the character set.
Unicode has its modifier characters, of course, but it doesn't force their use and instead falls back on things like normalization forms. My goals are different, though, so I'm free to make them required. They only look right atop 5-pixel-tall lowercase letters at the moment, but I've got ideas how to handle that.
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