Ah, I'm not surprised they did something more rigid with it in Neverwinter. As best I understand, most themes are not attached to a background - I certainly can't find any mention of it in Darksun, where they first showed up. The real point is,
technically HeroLab should allow you to select multiple backgrounds for a character, and then require you to choose the benefit from only one of them.
I always figured the HL devs left it out because it's a pretty unimportant aspect of character building - there's no reason you couldn't just write in additional backgrounds, if they don't need to have a mechanical effect.
In any case, these changes look really exciting, and it would be super awesome if you can post the patched files like last time