Guys from Kemper have been super helpful and overly patient with me. Thanks for that.
Turned out the Direct Amp and Merged Profiles had been done at different times, a day apart in this case which could have changed the amp state according to Kemper (tubes state, humidity, warming up of amp etc..). There was also different noise gates levels and the gain on the DA was slightly higher. So those are not apples to apples comparison.
After adjusting I can say the DA and Merged Profiles passed through the Kone with same Imprints are quasi identical albeit for a slight different of tone that could well be generated by the differences in the way the different sessions were done.
All that to say that in the future I will make sure that whatever DA I get in a bundle, they all come from the same sessions as the Merged Profiles. I have packs where DA are months apart from Merged...