Scotland's and England's interests haven't aligned for a long time.

One might say ever. England had a thing about keeping as many countries under their sovereignty whether they want it or not. (They are kinda like Europe's China in that sense) Scotland just got tired of fighting war after bloody war and an economic partnership became more attractive than fighting and dying in vain for an independence that might never happen.

The Scottish identity has been maintained as a separate thing from their place as a member of the UK. Whenever the subject of separation comes up, it has always been Scots that want independence and England not wanting to give it to them. Not recognizing them or their culture or their national identity, but at the same time making a point of depreciating those.