This in NOT a bug in Gentoo, rather the upstream's slip-up. When I looked at 3.0.33 tarball, I was surprised, that its size almost doubled from 3.0.33. It seems that whoever done the packaging has forgotten to clean before packing. I'm not sure how many files were duplicated, but at the very least docs-xml/output/ and docs/ seem to be (docs-xml/registry and docs/registry too).
I've entered it here, instead of upstream, as it would be better if the person, who complains upstream is a samba user (as I don't think I've ever used it, I just keep it just-in-case)
I suppose this is no longer an issue with 3.0.35 and 3.2.13 So closing, reopen if the newer versions have the same problem
