i think the default should be changed, but user-specified affinity
shouldn't be considered an absolute rule, just a preference. i'm
not
sure i understand exactly what sort of issue you're envisioning.
I assumed there could be issues since pset(3) is restricted to the
superuser (as well as pthread_setaffinity_np(3) now), but when
rethinking about it I admit not seeing a problem as non-privileged
processes cannot change the process priority beyond their class'
priority.
The only other case that comes to my mind would be a dmover(9) like
system eventually reserving processor(s) for dedicated tasks, but I
guess that in this case the reserved cores would simply be made
unavailable in cpuctl(8)/pset(3)/etc...