Steam – civ6 patch not updating

As per this article on Wikipedia, downloadable modifications from Steam for Civilization 5 aren't supported on Mac's.

They're essentially the same, but the command line version is that: a more compact command line version that won't require any gui and therefore no window system to run on the server. Since you're running a Windows machine, I wouldn't expect any significant differences, but the command line version should use less ressource in case those are a concern.

Edit: In case you'd like to manage your server through a terminal (like SSH), the command line version would be the one that's easier to use (since it won't require any gui interaction). If you're using some kind of remote desktop connection this doesn't really matter either.