I find if I use the android app Poweramp (or the iOS app Onkyo HF Player) to play my music then I can use their built-in equalizers to pull out the harshness a bit between 2 and 4kHz. The bad sound returns when I go back to the radio which confirms that it is the built-in sound system that has the peaky roughness to it. The apps must bypass the car's sound engine. Disconnecting the car's centre dashboard speaker helped soften the sound too. But for a flagship model the Skoda engineers should have spotted this unwanted resonant upper-midrange sound peak and fixed it with a software update.

Re-opening this slightly old thread, I am completely underwelmed by the Canton system (which is connected to a Amunsden) on my MY18 Octavia VRS.  I frankly get better sound by enable Skoda Surround on standard speakers. 

 

 

You'll never be able to fix the upper midrange hardness on the radio channels. It's like a built-in peaky distortion that is impossible to tame with the limited Skoda EQ controls. Setting the audio focus to "front" is about the best compromise, and have the subwoofer on maximum volume, with all balance and front/rear controls at centre. The only fix for me was to prize open the dashboard centre speaker grill and disconnect this completely, and then play all my music through a free music app with a built-in equaliser to pull out the offending 3.5kHz frequency. For iOS I use Onkyo HF Player and for Android the Jet music player, both free.