Its not unfair because Referenda are only called for things of great national importance that seriously alter the status quo and are too big for a bunch of 650 people who happen to be in parliament at the time, to make a decision on.
The high bar is (Or was) deliberate exactly so a vote by 25.2 % of the population couldn't foist something on the other 74.8% who didn't want it.
you make the point yourself, it wasn't the majority of scots who voted for devolution it was 51.6 % of the people who actually voted. That works out at something more than 32% of the population. And that minority making a decision that would affect the majority is exacly what the high bar was intended to prevent. Tony Blair took the % requirement out because he had promised the Welsh Labout Party home rules (Being at the time the assumption that welsh labour votes would ensure the new parliament would be labour controlled.)