Isn't that just a manual workaround to get around the lack of automatic UI? I mean would you still rename them with <system name> if it was showed with system name prefix where you wanted it?

Not really. I could name it anything. For example, one comet in my current game is called Hadano Naval Base. so it would look odd to have Hadano - Hadano Naval Base. I couldn't just call it 'Naval Base' because that would be a problem in other windows - such as events. Plus it uses up space, so depending on names, it may not fit.
Either I add a system column for everything and make the other columns narrower, or leave as is. Right now, if you want a system name, you can include it. Adding a system prefix takes away the choice and flexibility - unless I also add a checkbox for adding the system name, etc.