Other ebuilds put vendor configuration into /usr/share/X11/xorg.conf.d; /etc/X11/xorg.conf.d is apparently for system-specific configuration.
+ 04 Oct 2011; Lars Wendler <polynomial-c@gentoo.org> + xf86-input-virtualbox-4.0.12.ebuild, xf86-input-virtualbox-4.1.2.ebuild, + xf86-input-virtualbox-4.1.4.ebuild: + Fixed installation path of 50-vboxmouse.conf without a revbump (bug #381035). + Thanks for the report.