Hey Mpesta, don't know if this still interests you but it's definitely still relevant to me as I just bought a stomp xl and am discovering the same problems with the katana 50 mkii. As you say "the final possible volumes of the pre-amps to be widely off" and I can't help but find that all the preamps going into the katana power amp basically all give a clean tone. It appears that one must use the amp-amp block rather than preamp-amp block with the katana's power amp in although I'm not entirely certain of this as I can't find a reliable source on this and am basically having to use my ear.
Have you worked out the reason for this since you posted it last June?
The Katana manual block diagram appears to suggest that you only need the preamp-amp block as the 'power amp in' obviously skips the pre-amp section and goes straight to the power amp, but as we've discovered that sound really strange.
This video seems to suggest that you must use the amp-amp block and are free to turn IR/cab on or off as you please.
https://www.youtube.com/watch?v=GER1TP3Xutg&pp=ygUYcG93ZXIgYW1wIGluIGJvc3Mga2F0YW5h
Would love to hear if you've had any further thoughts or developments since postin your question Mpesta! :)
