I am just guessing what the Kemper is doing below. I have not played around with PURE CAB much.
When you mic an amp, you will not get a perfect sound without some work. The mic will not only pickup the speaker but also any reflections in the room. You will also have sounds hitting the mic from different parts of the speaker at different times. If you have a 2x12 or 4x12 you will also be getting sound coming from the additional speakers which are a further distance away and will be delayed/out of phase.
The reflections are never in phase with the original sound. Sounds that are "out of phase" will reduce the volume of a particular frequency. This creates little suckouts in the frequency response. The higher the frequency the more change an out of phase signal will do to the speaker signal (due to the ratio of distance traveled to wave length).
If I were to write a PURE CAB algorithm I would first look at the freq spectrum of the IR. Then I would try to average out any fast dips/changes in the response. These would not normally come from a speaker but from mic phase issues in the making of the IR.
Having suckouts may be a critical piece of a high gain tone due to the high amount of harmonics in the signal. That is why the manual states PURE CAB may not work great for high gain stuff. With a clean tone, large changes in the IR are not as noticeable.
The manual states that PURE CAB affects badly recorded IRs more than good IRs. I take this as "We cant fix what isnt broken". If there are no suckouts to fix, we wont do anything.
Like I said, just a guess. The first time I made a sweep of my 2x12 cab, I was blown away at how bad the suckouts were. It took a lot of blankets and foam to clean it up.
If it sounds like it is being played thru a tube, it has suckouts. It is amazing how many speaker IRs from big companies sound like they are in a tube. You would think they would make the IRs in a single speaker cabinet filled with sound deadening material while being in an anechoic chamber to reduce any outside reflections. Or use Room EQ Wizard to record several sweeps and average them together to make the IR. Amateurs