Why does C&G not have a colored outline on the top of the box like say prosperity 2e?
In the words of Wernher von Braun, "that's not my department." It's nothing I knew existed, would have known to proofread for, care about.
What is the recommended way to mark which card is the bane?
It looks like the original rulebook had no such recommendation. I personally just put that pile next to the Young Witch pile on the table, and in my experience everyone will remember. If you need more you could mark it with the Young Witch randomizer card (or any randomizer card, since there aren't more of these).