The question of whether a 'mandate' exists for manifesto commitments is silly I think. The SNP and the Greens (along with the Alba party but they got no seats so are irrelevant) both stood on a clear position that they support a second referendum and collectively they have a majority in Parliament to pass a bill for one which is all the mandate you need for something. Especially for a referendum where the key question is one where you are seeking a mandate directly from the electorate anyway. The electorate knew who they were voting for when they voted after all.
Fwiw, electoralcalculus always has the western bit of Caithness and Sutherland (Lairg, Lochinver) as more Lib Dem than the seat as a whole.
Electoral Calculus numbers are voodoo maths even when they have a solid set of local elections to base them on: in the Highlands where every local election is almost exclusively Independents with a few SNP and Green candidates standing in scattered wards it is even more so since they can't use local election results to test their hunches in the same way.