It is because of issues like this, and a few other things, that I have started to work on my own character creator program. [One reason is so that I can show a prospective employer an example of my C# skills]
How I am doing it is by having a level above "Setting" for "Campaign". I cannot tell you how many times it would be great to pull an edge or two, or some hindrances, or anything from other settings without taking the "All or Nothing" approach. As Hero Lab is currently configured, we have to take ths source and preclude everything else. And as stated earlier, it can be hard to figure out what that even entails.
The way that I am designing it there is no need to tromp around with the editor. I have found that tends to intimidate people. Instead it is a tree of a bunch of checkboxes and sub-menus. You can go to the book that you want and either "enable all" or enable things selectively. The Configure Hero settings does this, but this would take it one step further and gets into the individual details as selectable.
I want to be able to click on "Joe's Deadlands Game" and be done with it as it changes all of the other settings for me. In the meantime I have just made a "default character sheet" for each campaign with all of the correct settings. It works, but people have to remember to not save over it.
Savage Worlds is not confined by the core rule book. It is actually a very open-ended game system. There are many things that are immutable with Hero Lab but instead should be able to be opened up for alteration. Many of these things I have found hacks to get around, but they should not require such hacks. The ability to have options should have been built into it from the beginning.
What bothers me is that many of the things on the feature requests are really easy to do. Hero Lab can be made to do so much more.