Music, Keyboard Maestro, Better Touch Tool, Hazel, I could literally list out at least 20 more. Indigo is not an app you use. The UI is purely for configuration. Once my server is running, I expect it to run in the background while I do my development work. When I am done, I would open the UI window back up and stop it. Or quit the app if I was completely done.
It's like the Music app. How annoying would it be if it quit when I closed the window? I don't need the window open to listen to the music. I don't need the Indigo app open whiles it's serving up my web server.