Its more of a fundamental scheduling issue. The unlike big/little cores OS has no idea what apps "prefer" cache or frequency.
From time to time, it can retry the test, because software frequently changes what it spends time doing.
I wouldn't be too worried about this personally, as configuring the few really sensitive apps with ProcessLasso or Aniancy is pretty easy.
Factorio players don't necessarily know anything about computers. And you don't know if they bought this CPU or if it came with their fancy prebuilt.
A properties page for the executable with a checkbox for “favour stacked cache cores” or some such.