That would be the case for me. I found PowerAmp sounds poorer on my Z1060. You can say it's slightly warmer, but to me it's muddier. It's a lot more obvious when I tweak the bass. The distortion was obvious enough for me to ignore, it muddy the sound quite a bit for me. I'm using both sony ex-1000 and IE-80 by the way.
To me it's the Clear-Bass that is keeping me from using anything other than Sony Walkman. With the Ex-1000 which shines in the treble and clearity, it lacks just a little bit in the bass to my taste. With Clear-Bass to be +1, it rocks my world. No distortion what's so ever that I could tell. I sink in the sound easily for hours listening to Armin van Buuren's A State of Trance. Using PowerAmp, no matter how I tweak the EQ, i couldn't find the sweet spot of that satisfaction. Worse, as mentioned above, little tweaks in the Bass in PowerAmp make the sound muddy to me.
Normally I use IE80 though. As it's a lot easier for listening outside home. Easier to carry and put on/off etc. With IE80 I normally just set the treble to +1 in the stock player, no clear-bass is needed. The sound feels "silky" to me with IE80, though not as "clear" like with the Ex1000. But good enough for me for listening to music on the go :)