I've been using a manual update process with my 2 machines. On my HP desktop today I was prompted to keep my existing or update /etc/systemd/system.conf. The default was to replace it. I decided to replace it but not before I made a copy of the existing. After the update completed I checked the difference using
diff /etc/systemd/system.conf ~system.conf.org there were no differences on this machine.
Note this is not from scratch Ubuntu Mate 16.04 install, but rather an Ubuntu 16.04 in stall with the MATE desktop added.
commands used - ls cp sudo diff
Link to full tutorial