Don't know about your Thomas, but on my Blue Bird the chair rail is formed by folding the sheet steel. So cutting off the rail means separating whatever is below it from whatever is above it.
On mine, what's above it is the thinner silvery textured sheet steel. My guess is that the chair rail material and the silvery material together make up some structural value. So I would not want to completely separate the two by slicing off the entire rail. But notching it -- no worries, I'm certain. But again, I'm talking about my Blue Bird.