I tested tracker 0.6.6-1ubuntu5.1 from proposed and I can confirm that it fixes this bug. It is no longer activated by gdmsetup. Directories like /root/.cache/tracker, /root/.local/share/tracker and /root/.config/tracker are no longer created when launching gdmsetup, unlike version 0.6.6-1ubuntu5. Gdmsetup seems to work fine, and tracker was able to find files in my home directory.
I tested tracker 0.6.6-1ubuntu5.1 from proposed and I can confirm that it fixes this bug. It is no longer activated by gdmsetup. Directories like /root/. cache/tracker, /root/. local/share/ tracker and /root/. config/ tracker are no longer created when launching gdmsetup, unlike version 0.6.6-1ubuntu5. Gdmsetup seems to work fine, and tracker was able to find files in my home directory.