You don't want to totally discount clock-on-the-wall time. Time used to wait w/o another thread ready to utilize CPU cycles may make one piece of code less desirable than another. One set of code may take some more CPU time, but, employ multi-threading to dominate over the other code in the real world. Depends on requirements and specifics. My point is ... use all metrics available to you to make your decision.
Also, as a good practice, if you want to compare two pieces of code you should be running as few extraneous processes as possible.