Can I be frank? I do not think the general population of the UK are sufficiently educated (or indeed sufficiently interested in doing actual research) to take complicated decisions of the type you are referring to. It's that simple.
We are a Parliamentary democracy. We pay people (quite a lot of people) quite handsomely to do the complex and detailed stuff that is necessarily behind sensible decisions on this matter. In my view, they should do that job. That is what they are paid for.
So, in the case of Scotland, if a majority of Scottish MPs are SNP and take the view that Scotland should be independent - fine.
Similarly, in the case of the UK, if the majority of MPs support Brexit - fine.
However, I do stress I would want PR voting established first, because at present a minority can elect a majority, which is plain wrong.
To draw an analogy, referenda are like asking the crowd to pick the team instead of Pep. The only difference is that in that case (picking the team) it wouldn't really matter. So I would be much happier to go for that (ridiculous though it would be!) than go for a vote on membership of the EU, or NATO, or the UN, or whether we should maintain diplomatic relations with Russia, or the 1001 other complex things you could potentially have referenda on.