Is there any reason not to suspect that this was a noble's khipu made from a commoner's stolen hair?

Yeah that’s exactly what I immediatly thought, stolen or bought. It is common today that some people sell their hair to make wig for rich people

Or that this particular noble was a "health nut" and stuck to a commoner diet. Or was simply allergic to corn.

or a noble's message written on behalf by a commoner 'scribe'

This article is a case study of non sequitur