That's the theoretical reason why they shouldn't cover all discovered items. However, ATLAS presently times the kernels in order to be able to produce a comprehensive SUMMARY.LOG, and these timings could be skipped, assuming this functionality were added to the atlas install process.
There are some weaknesses of architectural defaults. One of the main ones is how they can go out of date, and cause slowdown. One big way this can happen is with compiler changes. For instance, gcc 3.0 produces completely different (and inferior) x86 code than the 2.x series, and 4.0 was similarly worse than latter-day gcc 3. Almost all architectural defaults in ATLAS 3.10 were compiled with gcc 4.7.0.
Anytime a different compiler is used, the architectural defaults become suspect. For truly inferior compiler (like gcc 3.0, 4.0, or 4.1), there is no way to get good performance, but at least some problems can be worked around by having ATLAS adapt itself to the new compiler, and architectural defaults prevent this from happening.
Clint Whaley 2012-07-10