The agetty manual page says: "All files with .issue extension from the directory are printed in version-sort order. "

But it looks like this is done per directory, so at first all files from /etc/issue.d are printed, afterwards from /run/issue.d and at least /usr/lib/issue.d

Is this really wanted? This makes it hard to get some useful order into it. And it would be nice if you could overwrite files from /usr/lib/issue.d with files with the same name from /run/issue.d or /etc/issue.d.