Oh, funny. So what I assumed "old" was actually "new" and vice versa. :-D Updated to latest master commit and now files are installed to version_2. Downloading the latest version_2.tar.bz2 now also matches what is in the git repo (structurally). Thanks!
OK, I try to clarify: When filing this bug I was using a lensfun version based on git master branch commit 385aa1 that I installed a couple of days ago. This installed the included xml files to /usr/share/lensfun/version_1/<files> When running lensfun-update-data this morning it correctly recognized version 1 and downloaded http://lensfun.sourceforge.net/db/version_1.tar.bz2. This file was then extracted to /var/lib/lensfun-updates/version_1/<files> In these updated files in /var/lib/... attribute...
At the time of writing I was using commit 385aa1. I now updated to latest master 0ec0c3. This also includes the latest version of the xml files in /usr/share/lensfun/version_1. They do not contain the above change. Using lensfun-update-data will of course not download anything as there is no newer file on the server. I still had a version_1.tar.bz2 file (downloaded an hour ago) lying around and unpacked it to /var/lib/lensfun-updates/version_1 manually but they seem to be ignored (timestamp?) or...
lensfun-update-data breaks lensfun