There is one major difference - and before I start - my comments here are meant to be constructive, not defensive (or offensive).
Tone Matching a recorded guitar tone (via Axe) works awesome. Sounds perfect. Love it.
Tone Matching a raw amp (to then play through a SS amp and 4x12 cab) - VERY different outcome. The Axe still needs 'tweaking' to accommodate for some unknowns (which is the power amp's reaction with the cab). So you must dial in the Speaker Impedance Curve settings to get the Tone Match to sound right. I have spent hours playing with advanced Amp features to try and get my Marshall rig sounded identical in the Axe. Its VERY close, but I've put a lot of time in.
The QC and Kemper somehow 'guess' on the Speaker Impedance and they seem to get it closer. I know that is going to trigger some folks, but that has been my experience. I mentioned earlier - the Wizard capture I did. The QC capture with a quick adjustment to gain and low end, was near perfect. I could not get the Axe to respond the same way.
Is it pilot error? Probably - but that's the point. I consider myself a very experienced pilot. I've been a Fractal Fanboi, and have gigged with nothing other than Fractal, since I got the Ultra. I absolutely love the products....but if I'm being as unbiased as I can - the Tone Match is not very good for matching a raw amp, UNLESS you plan on spending some time in the advanced amp features, filling in the blanks that cannot be captured during the Tone Match process.