class system differs from upstream (has an "undefined" permission where upstream has "start" and "stop"). I think Dominick raised the latter as an issue on selinux list a while back and noted that an attempt to add "start" and "stop" to Fedora policy in an update broke systemd, but IIUC, that was because they were defined without allowing them to any confined domains.
This bug appears to have been reported against 'rawhide' during the Fedora 25 development cycle. Changing version to '25'.
selinux-policy-3.13.1-208.fc25 has been pushed to the Fedora 25 testing repository. If problems still persist, please make note of it in this bug report. See https://fedoraproject.org/wiki/QA:Updates_Testing for instructions on how to install test updates. You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2016-662487f8f1
selinux-policy-3.13.1-208.fc25 has been pushed to the Fedora 25 stable repository. If problems still persist, please make note of it in this bug report.
It appears that you synchronized the class system permissions to match upstream (thanks for that), but you kept the "undefined" permission definition (just moved it to the end). Is that permission actually used by systemd? If not, the libsepol update to only warn instead of fail if the permission is not resolved should allow you to remove it altogether without breakage.