I think that we, as a people, sometimes "over think" the simplest of things. One of those things we over think is how our name is spelled, and what it means vis-a-vis clan association. The simple fact is that in the 17th and 18th century many Scots either dropped the "mac" from their name and added "son" to it (Macdonald becoming Donaldson) or discarded it altogether, as in McDonald becoming simply "Donald". Skene, writting more than 175 years ago, was well aware of this, living as he did at a time when within living memory many people had adopted new variants of their traditional "family" name by Anglicizing it.

Unless there is incontrovertible proof otherwise, I would tend to say that the simplest explanation is most likely the correct explanation.