Comment 12 for bug 159371

If you do insist on having a different motd, though (which I think is unwise; it's not uncommon to run small-scale servers by installing a desktop and then sticking a few server packages on top, and people logging into those servers might want help too), then remember that resolving conflicts among packages is always much easier if you don't try to cram everything into the same file. You could have /etc/motd.tail.d/ and have /etc/init.d/bootmisc.sh concatenate uname information, followed by /etc/motd.tail, followed by everything in that directory. This smells somewhat of overengineering, but I don't see how else to fulfil your requirements.

With regard to motd.md5sums, this should clearly be updated to match all versions of that file that have been in Ubuntu. That could be done retrospectively. However, you still shouldn't edit it at runtime; the handling of this file is complicated enough already without trying to have it be controlled by multiple packages at once.