No, this is still the same. The theme modifier for custom homepages overrides the site setting entirely. Navigating this is a little complicated because if a site has multiple themes available, and one doesn’t have a custom homepage, we’d have to manage fallback. Something for us to consider.
Not yet… the options are still the same as top menu anyway, but one thing that did change is that default will always be available in user preferences now (previously it was conditional). “Default” in user preferences will follow the site setting.
Also a “not yet” here too — outside of a custom homepage in a theme, the homepage of a Discourse site still has various requirements about being a topic list page (or /categories) and api.addNavigationBarItem() has much looser requirements.