I noticed recently while modifying my /etc/passwd and /etc/shadow files that the 'portage' user (UID 250) is listed in the former, but not the latter. Checking the latest available stage3 for my architecture (stage3-amd64-20160901) reveals that the problem still exists there. It doesn't appear to affect anything (emerge still runs without any issue), so I'm not sure how much of a problem this is, but I imagine it's probably still something that should be fixed. Reproducible: Always This probably extends to other stages/architectures/profiles, although I've only checked the regular amd64 stage3.
*** This bug has been marked as a duplicate of bug 521970 ***