Mixing code and content leads to all the most common injection-style vulnerability classes: buffer overflows, XSS, SQLi, command injection, etc. Fundamentally, I believe this is at the heart of the problem. The paper does go on to address this:
> Another proposed theory blames John von Neumann's stored program concept [15] for the woes of arbitrary code execution; the fact that data and program in computers are stored on the same storage medium may allow an attacker to illegitimately modify the program rather than the intended data [10].
From there it provides ROP as a counterpoint to the "stored-program hypothesis." This makes sense because ROP allows one to achieve arbitrary code execution without necessarily modifying the code. Although, while I agree that mixing code and content may not be the highest level abstraction for concern here, I do think it's often a fundamental flaw from a practical perspective.