I actually turn the input level way down in Helix Native because it distorts otherwise.
It also distorts with other PC based amp models like Blackstar St James. Have to turn the input on that down too.
Edit:
I just tried everything I could. Set the input to the HX Stomp to Line, Guitar Pad ON, Put a gain block on at the front of the chain set to -12db. No success.
The only way to describe it is: In Helix Native on a clean preset like Double Vib, If I run my fingernail across the strings I can hear the nail. Can't hear it on the HX Stomp. This guitar has slight fret buzz, I can hear it come through on Helix Native. Can't hear it on the HX Stomp. The upper detail is just gone.