There are several subdirectories under /etc/texmf/ where ebuilds could place fragments of configuration files to be included in a single file by texmf-update. Unfortunately right now these files are CONFIG_PROTECTed, so unmerging an ebuild does not remove its configuration. I don't know for all of them, but at least updmap.d should be included in CONFIG_PROTECT_MASK, as you either have the font installed or not, there is not much of a configuration you would want to keep when the package gets unmerged or updated. I suggest extending the mask specification from /etc/env.d/98tetex to the following: CONFIG_PROTECT_MASK="/etc/texmf/web2c /etc/texmf/texmf.d /etc/texmf/fmtutil.d /etc/texmf/updmap.d"
This is not a bug. It is perfectly okay and sometimes desirable for a user to alter the files in /etc/texmf/{*.d}. And such a user won't like to have his/hers modifications overridden on the next upgrade. You can add those dirs to your own CONFIG_PROTECT_MASK in make.conf if you like.
