Regional "winner takes all" is pretty undemocratic - it's one reason Trump got elected in 2016 despite having far fewer votes than Clinton.
I think the answer for referendums is a presumption in favour of the status quo - such as requiring 50%+1 [edit: of the whole electorate] in favour of change, on the fairly reasonable assumption that anyone who can't be bothered to vote is content with things as they are. And if the nature of the change isn't clearly defined, as Brexit wasn't, then it either needs to be defined before the vote or put to a second referendum against the status quo once details are known.
My post was more to highlight that if you were doing regional votes you'd fall into all sorts of traps of it being fair/not fair and even if you tried to make it fair you'd still end up with the same result as we had.
50%+1 of voters would be a fairly high bar, much more so than 2 thirds of votes, as many elections (at least for monitoring stuff) don't reach 50% turn out.
Although in the case of Brexit (with a circa 75% turnout) it would have also been about 2 third of those who voted.
Can we therefore take the 15 million or so non-voters in the last General Election as de facto Conservative voters then?
No, because at the time of the election technically there are no MP's, there's a load of former MP's being ministers and running government. As such there is no voting option to maintain the status quo, as such there's no place for those abstentions to be added to.
That's not the case for a vote one way or the other, as voting for an MP is voting for person A, B, or C but with no option to vote not having any of them.
To give an example, let's say I was offering a vote on should I sell my car; there's two options yes or no. You can sell it voting for selling my car or voting for keeping my car, however you can't vote for doing neither.
However I was to offer you a vote on what new car I'm going to lease (having returned my old lease car) then the options are for one that's the same make and model as I've already got or a choice one of another few options. There is no option of being given a random model of most popular make last year (effectively a Tory MP).
Also, whilst it's a general election, the status quo isn't the Tory government. What we vote for is a local MP. Once that vote has been made the winners of those votes go to London to try and form a government. As such the status quo votes (SQV) would only be for the last MP.
That does get us into an interesting question, what happens when an MP defects? Did we vote for them and so the SQV go with them, or do we vote for the party and so the SQV go to the new party candidate?
Likewise what happens when there's boundary changes or a new seat is formed? Where do their SQV go and how do we know if there's any SQV or not from those changes?
The idea of SQV is a bad one.
At least with meeting a fixed target for change to happen, but with a guaranteed future vote if the fixed target isn't meet but also isn't voted down by that fixed target (say until leave or remain reached 66.6% there would continue to be votes on the matter).