From what I have read I believed that the Scottish highlands were very culturally different to the lowlands. In fact, they were descended from different tribes. The highlanders being descended from the Picts and the Gaels, which produced the "Scots", and the lowlanders being a mixture of many peoples including the germanic tribes that conquered England and even the Romans. They even have a different language: Scottish Gaelic is celtic language native to the highlands and the "Scottish language" is a Germanic language native to the lowlands. As such, the lowlanders did not have a clan system and looked down on it. If I understand this correctly, why then do I sometimes find references to "lowland clans" such as the Douglas or Campbell clan. Is it because both regions had the clan system but the lowlanders abandoned it after the middle ages, whereas the highlanders used it until the highland clearances? Was a lowland clan simply a family?
I can't give a reason as to why specifically different terminology has been employed, but I'm familiar with family organisation in the Borders due to my work on crime in the sixteenth century.
You're right that the cultures diverged somewhat over time. From the twelfth century, increased Anglo-Norman influence brought the Lowlands more in line with the rest of Britain and continental Europe culturally and socially. That said, family was still quite a strong organising principle throughout Scotland well into the early modern period.
So what you'll find in the Lowlands (more particularly the Borders) is the concept of 'surnames' (Rae, The Administration of the Scottish Frontier, 1513-1603, 1966). These were similar to clans in that these were kin groups based historically in particular geographical areas.
You tend to find the concept of surnames associated primarily with bands of reivers and particularly troublesome families like the Armstrongs, Maxwells, Johnstones and Douglases. This accounts for the crown's attitude towards both the Highlands and the Borders as wicked, chaotic or lawless regions. These areas were quite remote from Edinburgh and often difficult to manage through messengers and direct royal oversight, so local customary justice and clan or surname politics tended to have more sway over life in these regions.
In Central Scotland and the Lowlands north of the Borders, urbanisation was more widespread and, although kin was still central to social and political relationships, it was not necessary to rely on family for protection and order to the same extent as in the more remote regions of Scotland.
It's quite correct to refer to Lowland family groups as clans, but more often they are referred to as surnames and it tends to be in the context of border crime and culture.
Why the different terminology, I'm not entirely sure. The clan system was not exactly looked down upon. Rather, as the cultural and social differences (religion, language, justice, economy) between Highlands and Lowlands grew over the years, the Highlands came to be considered a somewhat "backwards" or uncultured region and so too did many aspects of life in the area. It was also problematic for a government and monarch that was ever trying to centralise to have men making bonds and oaths to heads of families as it undermined the authority and importance of the crown. The Borders, a site of conflict for generations, was likewise considered unruly, if not barbaric.