See, when you actually do the backup, not "overwrite" the existing one. What it does is, once the new copy is complete, delete the old.
That is, temporarily, in the two copies are iCloud. And 3GB + 3GB 6Gb => 5Gb. Basic Mathematics.
The reason is simple: what if overwritten and while the new copy is made fails (you drop the network, for example) ?. Copying iCloud would corrupt. :)
This so broadly. I guess (and I believe) that Apple has a more sophisticated system. But based on the last backup I made to pass iOS8, gives me that's how they work (or very similar)