[UncleMeat]

No it isn't. The paper forces the universal turing machine to execute a different machine than the one on the input tape by providing crafted input to the intended simulated machine. It isn't a joke paper.

U is fed machine T and input I. By only changing I you can force U to execute a different machine X.

[qsort]

Sure, but you achieve that by specifying I in a way you aren't really supposed to. You are effectively invoking undefined behavior.

The implications of this are well understood. You'd have similar vulnerabilities if you ran raw machine code on, say, an x86 processor. Enforcing checks and sanitization in such a way that the 'exploit' can't happen is the exact kind of job you'd have to do in order to write an operating system.