So...I've bought limited edition rockstuds and they came in a red box with a red dust bag. Bought another pair of limited edition ones this years and they came in a box with the pattern matching the pattern on the heels and white dust bags. Three days later, I bought a pair of espadrilles and they came in a red box with red dust bags. I think it just depends on the shoe and the season. I also have a pair of limited edition sneakers with a funky box but it's still a red dust bag.
Edit: Also, sometimes the SA will switch the dust bags of shoes. So if you were supposed to get red, the SA might have just grabbed cream/off white