>> The timing could be off between cores leading to some execution times possibly being inaccurate?
Precisely. Apparently, clocks aren't synched between cores and no correction is made for this.
>>And ballpark what sort of amount are we talking here?
I'd say between 5 and 10% but there's bound to be pathological cases.
I'd run both sessions (with and without affinity). Trust *percentage* values for ThreadAffinity = true; trust absolute and real-world performance values for ThreadAffinity = false.
And if there's major discrepancies between the two, be sceptical about specific ThreadAffinity = false values.
Profiling is more of an art than a science.