First time hosting a server. I wanted to clarify, what all pauses when you click the 'stop' button? My assumption is, all players are kicked off, dinos are frozen in time, and no time goes forward in game (as example stop it at day 3 12:15pm and stays there till you start back up server). Is there anything else, or anything I'm wrong on? 

In short, everything stops. It's as if the program were fully closed. The only exceptions would be if any mods track time passed externally.