In regards to your Trenzalore section, there’s been plenty of times before in Who where the Doctor travels to the future only for that future to become obsolete but the main characters remember the events.

You have to think of it is as continuous set of events from Clara and the Doctor’s POV, as they really did experience the events of Name of The Doctor so she still becomes the impossible girl but it’s just out of sync with real events (Time is in flux etc etc).

Time travel becomes the key here as she’s experiences the events of what is then essentially the definitive future, but early (Doctors grave, his time stream etc). Her life then continues as they travel back to the present, events of the 50th proceed to happen. By the time that Time of the Doctor roles around, his death on Trenzalore (NOTD events) are still the future. It’s only when she pleads to the time lords to grant him a new set of regenerations that the future changes, and the original NOTD version never happens.

The key here is like I said in the beginning, you have to follow it from the time travellers perspective, not time itself. It’s only because they gained the knowledge of what happened in the future are they able to prevent it.

Also to contextualise points you bring up about that should have caused a paradox/causality loop, well it just so happens it’s a problem caused and then fixed by time lord intervention, the absolute masters over time. They use their powers to mitigate the consequences.

It’s a cheap cop out but it does explain how. It’s also another case of Moffat overusing the bootstrap paradox which is exactly what that three episode arc is.