I've ordered the Airboss in Amethyst to avoid the dreaded red logo. Not so much because of the in your face advertisement but more of the fact that I despise the color red which is funny considering my passport is red lol but hey that's why I have a passport cover lol. Haven't received my bag at the moment but that's because a friend is bringing it over from the US next month (I'm in Asia).
Another option to the black marker might be to use fabric paint which should last longer than the black marker. Fabric paint comes in a variety of "delivery" methods, one of them being in a marker form.
Just thought I'd put that out there.