For the average user it's much easier to run a program, click 'activate' and then play.
These things are lost if you don't go through the process of the installer.
Furthermore, the addon modified the EXE and CON files directly to get the product to be as professional looking as possible (this is why Sunstorm games were the only ones to have unique loading and exit screens). but remember that addon got sold to about half a million people (and who knows how many pirated), most of which have no understanding of how the file systems in Duke 3D works, nor should they need to in order to play the addon. Poor packaging is exactly why I just went ahead and set up my own packages for all the Duke add-ons, much easier and more user friendly than Sunsoft's lame BS.
Actually if you are running Duke DC on Atomic, you could set it up very easily to run just fine without interfering at all with the normal game, and they should have done this when they packaged it.
