As to the issue of removing /win, you do that so you don't play in a window. You can have 1280x1024 resolution (or whatever) and still play in a window. Most people don't like to play in a window, but a few do. For hosting a dedicated server you want it to be in a window, but otherwise it's just your choice. If you get rid of the resolution I imagine it will just use the last resolution that was saved from last session, or game default (640x480?).
As to the preferences, lets not bog down the thread with preferences. I mean in my opinion starting a server with a certain required number of humans just drives people away. Unless it's an organized tournament or something. That's why my JA server is constantly going. Set a "warmup" time (pregametime) and its cool for the people who join a little bit late. Keep the action going I say. Of course the beta's problem of dropping people at the map changes doesn't help any... but I know many people aren't willing to wait for others to show up.
Btw is there are a command for forcing team balance?