I see your issue more clearly after having a quick look at the Featured Lists component. One option is to refactor that component and have it output all of the lists into one Ember component. Then you could add that component to a plugin wrapper outlet.
Another option is to add a second plugin outlet to the custom homepage template, something like <PluginOutlet @name="below-custom-homepage"/>.
I may be hanging on to this custom-homepage outlet with a message for admins for not much good reason, to be honest. That warning is not all that useful…
Yeah, that can be tricky. In my local test just now, /custom there doesn’t work properly. It’s better to use /, that routes correctly. But it still doesn’t highlight.