The messages that pop up when selecting all 3 masters are normal/harmless. My recommendation: Check inside your morrowind.ini file and find the line with the "AllowYesToAll" option. Enable that and instead of clicking yes a thousand times, you just click cancel once to say "yes to all".
Those werewolf changes are part of something called the "Evil GMST".
To keep it short:
If you use only the morrowind master, the CS will add a bunch of useless references about the expansions, which you will have to clean up after him.
If you use all 3 masters, the CS doesn't add the references. If you're releasing a mod publicly using all 3 is not ideal, but if it's only for your own use don't worry about it and select all of them.