No guarantees about "all current mods", but I successfully tested a sample change in medkit prices (a strategic change) and unlimited ammo for the assault rifle (a tactical change) and both functioned correctly even with steam ONLINE. So, I am reasonably sure all mods will work. Yeah notepad will do that when saving a new file. Generally speaking, the way you fix that, is after saving in Notepad, you go to the folder and then right-click the file and Rename it.