I just bought both expansions and now I'm dealing with a ruleset option in which you get to choose gathering storm or rise and fall. Can't both expansions be activated in a playthrough? I'm a bit confused.

All mechanics from Rise & Fall, are included in the Gathering Storm ruleset. So if you want the content from both expansions, play the Gathering Storm ruleset.

yeah gathering storm contain all what you can found in rise & fall. and it is better ! :)

Great. Thanks!