I've heard of well known dealers separating kits as a courtesy to customers who need just the body or kit lens when stock of the single item is limited or unavailable.
If the dealer is reputable, it comes down to how important a picture on the box is to you.
Rather than fearing a sinister plot, consider the very real possibility that the friendly dealer wants to make sure you don't have to wait for a popular piece of equipment with its USA warranty. The white box is more common with kit lenses than bodies.
Keep in mind that some people, God knows why, are willing to pay more for your used gear if you have the original box and wipe the dust off it.
Is it difficult to find the new 5D in stock right now ?