"I don't think it is really right to compare the suppression of Border brigandry with the Clearances"
Actually there are real correlations between the two areas. As early as the mid to late 1500s the Scottish central authority was taking measures against what they described as "clannes in the heilands as weil as bordours". Both areas had seen authority break down and kin or group self protection become more prominent. In the Highlands because of the demise of the MacDonald Lords Of The Isles and the unrest caused by fighting over the scraps - and in the Borders due to incessant warfare and the smashing of the Douglas family. As soon as the border became fully peaceful then the new Scottish King of England brought central authority fully down on the warlike society the monarchs themselves had cause to be created in the Borders and he also then started to enforce central authority more seriously in the Highlands. Like in the Highlands after Culloden the Borders, despite the initial oppression, didn't see real rural depopulation until much later. If you look at population loss in the 19thC then Berwickshire suffered as much as anywhere. It is recognised that rural clearance happened over much of Europe and in the Scottish Lowlands it had previously beed described as 'improvement' rather than 'clearance'
The main difference is that the new industries set up in the Borders "ie mainly textile" were eventually a success and the existing towns expanded greatly whilst other new specially built villages like Gavinton and Newcastleton were also a success. In the Highlands the population was mostly moved to the coast to work on things like kelp harvesting subsidised by small crofts. The industry collapsed though and mass migration and emigration eventually resulted in severe population loss especially after the potato famine. Also the movement of people off the land in places like the Borders was almost certainly more gradual. In the Highlands it was sudden and the chiefs and other landlords were often heavy handed.