In character builder Eberron and D&D Home campaign are two separate options, but does choosing Eberron actually make any changes or restrictions (similar to those with the dark sun setting) in character builder? I ask because my players have rolled there characters in the default setting and I recently decided that the story elements of Eberron much better fit both their characters and the tone of the campaign I was going for.
Home Campaign is code for "everything goes"
All the other options are supposed to limit choices to ones either permitted (as Lair Assault and Encounters seasons may have regulation determining selection options) or suggested (Dragonmarks do not appear in cannon Forgotten Realms).
The only mechanical impact that I can see for selecting the Eberron setting, is that the background options are limited. For example, Forgotten Realms Player's Guide backgrounds do not appear as options (though Neverwinter ones do).
I would have expected that setting specific themes, such as the Dark Sun ones, classes such as the Bladesigner, deity choices such as Pelor, and a more complete set of setting specific backgrounds (such as the aformentioned Neverwinter ones) would also have been restricted, but it appears not.
From page 5 of the Eberron Player's Guide.
HOW TO USE THIS BOOK
This would seem to support all of our conjecture in the comments section. Thanks for weighing in everyone.