Of course it should matter! Which is why I’ve let the lovely Solomon blackwood tempt me back to wood for my Dave Copley keyed flute when I thought I was going for Delrin again and remained unmoved by the regular African blackwood. So go for the mopane if you think it’ll make you happy because it’s your flute and your choice…
Also (generically) prone to warping, which doesn’t bother some but upsets me (a wood I used to like but no longer trust!), though Casey seems fairly confident about the quality of his box…
Also, IMHO, his boxwood flute sounds better. I’ve played them both.
Both at the same stage of your flute-playing career? While working solely/mostly at them to explore and develop their capabilities without the potentially counterproductive distractions (different embouchures, bores, hole configurations etc.) of other flutes?