crossdev doesn't work with Gentoo Prefix at all, because all paths in the scripts are hard-coded. Upon calling the main script you get this error message: ~ $ crossdev --help /home/bblock/local/portage-tree/usr/bin/crossdev: line 18: /lib/gentoo/functions.sh: No such file or directory A quick glance into the script reveals fast at line 18 that this is no packaging error. Maybe this is by design and its not supposed to work in Gentoo Prefix, but then it should not be in the stable package set for Prefix. I tested this with 20160602-r1 and 99999999 (HEAD was 8b1b79e02cc36bc6f2b5583db6aeea333fb8d59b).
*** This bug has been marked as a duplicate of bug 384167 ***