This is one example where colour support in fonts would be useful. A useful addition to the OpenType specifications if any readers here have influence on such matters.
Out of scope. You can use markup to make characters red.
Something I have a vested interest in with my own focus on Ancient Egyptian Hieroglyphs.
Budge used to print a solid black line over red Coffin text and the like.
The answer to the original question about black a with red macron is:
You cheat, just like they did in the good old days of lead type. For that matter, just as they did when they had to put down one pen and pick up another.
You can't expect the encoding to colour elements of precomposed glyphs. -- Michael Everson * * Everson Typography * * http://www.evertype.com

