Own ebuild placed in /usr/local/portage are ignored by crossdev. For example, I placed an own ebuild for sys-devel/gdb in /usr/local/portage, because I applied a patch to make avr-gdb work together with eclipse. crossdev --ex-only --ex-gdb --target avr then emerges avr-gdb by symlinking /usr/local/portage/cross-avr/gdb to /usr/portage/sys-devel/gdb. Instead of this, the symlink should point to /usr/local/portage/sys-devel/gdb.
added support to current version