Why do Upstart jobs use `start on runlevel [2345]`?

Yes they are used for compatibility with other distributions and the LSB PDA specifications. I have had multiple systems in which runlevels 3,4,5 were used, but don't ask me what they were, this was years back.

If it bothers you, it shouldn't be an issue to remove those runlevels in all the configurations, but I would recommend leaving it as is. If it ain't broke, don't fix it.