Independence movement got a majority of seats despite having slightly less than 50% of the vote. but that still gives them the right to call a referendum. Weighting the seats with 2nd vote parties would only become an issue if their vote was to fall enough for them to lose the majority of seats. What happens in that case? They still have a mandate to call a referendum, but their popular vote is now lower and they will likely lose the referendum. Lose 2 referendums and independence is gone for a very long time.