In D&D Insider's character builder, both Eberron and D&D Home campaign presented as separate options when creating a character. Does choosing Eberron vs. "D&D" actually make any changes or restrictions (similar to those for the Dark Sun setting) in character builder? I ask because my players have rolled their characters in the default setting and I recently decided that our next campaign would take place in Eberron since its a much better fit for their characters and the tone of the campaign I am 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 canon 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 Bladesinger, deity choices such as Pelor, and a more complete set of setting specific backgrounds (such as the aforementioned 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.