That is not comparable, Turkey being part of EU is, I.e. EU gets to decide who is in EU providing there is democratic mandate from that countrys electorate.
It is entirely comparable - and mentioning Turkey isn' relevant as Turkey aren't part of the EU.
You suggested that the rUK should have a referendum that would over-ride the decision of Scotland in their own referendum (in your view that although Scotland voted to remain in the UK, they should be kicked out if rUK voted that way in their referendum).
So the exactly equivalent situation for the UK and the EU is that the rEU should have a referendum that would over-ride the decision of UK in their own referendum. So in this case even though the UK voted to leave the EU, they should be required to remain in the EU if rEU voted that way in their referendum.