Specifically, settings generally come with a list of new edges, hindrances, powers, etc. In addition to the new ones the setting provides, it often creates a list of disallowed items of the same type. It's part and parcel of the way the core rules (book) are designed.
(I'll talk about edges here, but it applies to all features that work the same way)
When dealing with the rules in FG, you upload the setting, which has all of the new stuff. You also upload the core, which uploads all of the core edges. This creates issues, as you now have both "updated" edges from the new setting, as well as the disallowed edges that came in from core.
As settings are designed to work with the core rule-set. I would like the setting to compile the allowed edges into one list that can then be shared with the players from the GM terminal.