Let's look at this logically for a moment.
* James Franklin Bolton fathered Isabella Belle Bolton and James Franklin Bolton, Jr.
* Isabella's death certificate says that her mother's name was "Martha Smith".
* James Jr's death certificate says that his mother's name was "Margaret Risher".
* Not only are the mother's last names different, but their first names are different as well.
* Has anyone considered the possibility that Isabella and James may have been half-siblings?
Also, just as you wonder if Martha's mother was the Risher, it is also possible that Martha was the Risher and that her mother was the Smith. That might explain why nothing else can be found to tie the Smith name to the Bolton name in that generation (just a hunch).
We moved in with my grandfather (Girard) and grandmother when I was about 6 years old (around 1972), and we either lived with or next door to them most of my life. I moved in with my mother and helped to take care of my grandmother after her last stroke, and cared for her until she died. While caring for her, my grandfather also lived in the house. I was at his side, listening to him reminisce about family and his younger years until about a month-or-so before he died.
One thing about my grandfather is that he insisted on his children knowing the names of their ancestors. He drilled my mother regularly on the names of ancestors and told her to never forget who or where we came from. He did the same to me and one story that he told was how two Risher sisters had married two Bolton brothers.
I am going to stay on top of this issue until I have found solid documentation to prove one way or the other. Until I have found that solid documentation, I am going to rely upon the information provided by my grandfather for his grandfather's death certificate, knowing full well that my grandfather knew who his parents and grandparents were.