The update is downloaded from your registration page.

There is just a single update file (found among the CC3+ downloads) that will update CC3+ and all the installed add-ons. It should always be installed last, and if you install a new add-on at a later stage, reinstalling the latest update is always a good idea because it might contain update to the new add-on you just installed.

The community atlas is described here.

Best approach here is simply to contact ProFantasy using the licensing question email listed on the contact page.

Explain exactly what you want to do, be precise, and explain the different scenarios (for example, making maps and distributing with the program is a different thing entirely from distributing tokens), and they will tell you if this is ok or not.

Users here cannot give you anything but their view on the EULA, ProFantasy can both give you the correct interpretation, as well as give you permissions where they are needed.

Second edition is the best :)

(Currently playing 2nd ed this weekend with my friends actually)

Looks like the display have been corrupted somehow, this is not normal.

Does quitting and restarting the program help (it should automatically reload the last open map)? If so, you have a workaround, but you should probably still contact support.

It is not possible to call such things from the command line. CC3+ wasn't written with batch processing in mind.

You can talk to CC3+ from an external program using the Intercom interface however, which means you can send commands from an external program which are then run as commands inside CC3+. I don't have a tutorial for that on hand. Some information can be found in this old blog by @saunderl http://cc3-developer.blogspot.com/search/label/Intercom

The second alternative is to make your own XP which opens up a lot of possibilities for expanding CC3+ with your own code. I don't think you'll be able to implement more command line options or prevent the gui from loading though, those things are (most probably) beyond what an XP can do.