Okay - so it's leaking from the cistern. I know what you mean, you have
a large plastic nut as you say which is supposed to act like a
compression fitting using the o-ring making a tight seal. You could try
replacing the o-ring and maybe a new one would provide enough of a
seal. Maybe you could try shifting the pipe a bit so the "misalignment"
manifests itself at the pan end rather than at the cistern end, which
might be more forgiving of the misalignment.

(In my experience the pipe at the cistern end has to emerge exactly
vertically for it to seal).

Don't tell anyone but what I have done under similar circumstances is
to wrap PTFE tape under, around and over the o-ring and up the threads
of the connector. Then tighten up the nut over the whole lot. It's a
bodge but it's worked for me. You can quite often see this done in pub
toilets where the cistern is at a higher level.

Moving the cistern could give you a major headache with the incoming
water and overflow connections so bearing in mind the cistern is hidden
I'd try alternative strategies first!

Luke