From my POV, it seems that NBT consists of two essential parts -- a template saving/selecting tool and a settings cloning function. Having worked with Cloner quite a bit, I'm guessing you're using the same basic functions there.
The main problem I have with NBT is that as a user I can't choose a theme after creating a site. As Super Admin I could clone the same settings into a users site, copying over the same theme, theme customizer settings and plugins used in the demo site into theirs.
So why not have this same option available to users? Couldn't NBT work as a plugin, doing those same functions again, but from within the dashboard? Sure, you'd need some decent warning processes such as "You're about to erase your current theme settings! Proceed?"
Possible? Not possible? I'm seriously considering hiring a developer to do this, so if there's something I'm not getting because I don't code, please let me know as I have limited resources (and about to jump up to full price on my WPMU subscription - yikes!) so if this could be a new feature from WPMU, that would be fantastic!