Well, if you look closely at the clouds to the left of the figure you will see the ghostly image of a coat of arms-- again, without the benefit of an x-ray, it is impossible to say with any certainty if these are the arms of Macdonald of Sleat, or of some other, unknown sitter.

To my mind three things are possible:

1) Sleat didn't care for the picture and it was re-done several times until he was satisfied;
2) The original sitter wasn't Sleat, and his portrait was painted over that of the original sitter;
3) This was a "studio canvas" with a generic nobleman sketched in, only to be painted over when a client was found who wished a similar style painting.

The arms are the intriguing bit-- Chalmer's father was Ross Herald (and a herald painter) in the Court of the Lord Lyon so Chalmer would have been au fait with Sleat's heraldry and in all likelihood would have included his arms in the painting, as was sometimes the practice of that time.

But, without the benefit of an x-ray, we will probably never know...