If we don't know about how sentient time-traveling machines work (hint: they don't exist), we also don't know how million year old eggs which look and feel exactly like the moon work (they also don't exist, but who cares?).
The consequences for Kill the Moon were all contained within Kill the Moon. There's no need for anything wider than that. Characters died, the world was put in peril, and people contemplated a terrible decision. We don't need every episode following it to be like 'hey, remember that time with the moon and then the thing happened?'. And I really disagree about Courtney. She was a fun character in The Caretaker, but she was much better in Kill the Moon. I think she really felt like a genuine person at times. She wanted to feel important, but she was overwhelmed by everything going on and just wanted to go home after seeing that. But when it came down to it, she stepped back in the action and realized that she wanted to be a part of the decision. This is a really good arc for a character to have over the course of an episode. Her character also worked pretty well for a metaphor for the people of Earth who had lost interest in space and finding out what was out there.
This is lyrical science fiction, the sort of which Doctor Who did back in the day, but has not really messed around with much in recent years (Gridlock kind of hit this mark a little bit). It's a majestic episode with some stunning imagery and amazing ideas, and it wraps it up with the faintest of science-fiction paints, but it's not concerned at all with the idea of if anything is scientifically possible. And that's just the way that Doctor Who should be. Warriors' Gate is full of things which are completely impossible, too, but that doesn't stop it from being brilliant.
In a sea of quirky characters, Victorian outfits, boring robots and spaceships, and worn out premises, Kill the Moon stands out apart from the crowd. It does things that are only possible to do in Doctor Who, and it doesn't care at all about what anyone else is doing.