Pure conjecture on my part, but I think your last assumption is correct. Being a Lowlander, if this is really pre-1900, he likely had no experience or knowledge of wearing kilts. I see several other details in the photo that suggest this is a makeshift pseudo-kilt outfit by someone who could only approximate the look. Although I do tend to question even the date of the photo. That's pretty good quality photography for the 19th century. Has this image been digitally cleaned up?

Cool family history, nonetheless.