Hi,
I use my Helix Floor, Helix Native and Logic Pro on an almost daily basis and have to say that I have not experienced any audio distortion, other than that produced by the specific blocks in Helix. Also my Kali Audio IN-8 2nd wave monitors are connected to the XLR sockets of the Helix to provide zero latency. I have been working with this system since buying my Helix in 2015 and adding Native when it was later released.
I usually record the processed audio from the Helix into a stereo channel on USB 1&2, and also a DI dry signal on another channel set to USB 7. The DI can then be used to re-amp the part after the fact (eg: if the processed audio has too much reverb it can be corrected).
Recording your signal at the correct level will help to avoid any distorted audio, as noted by @silverhead in the post above, you may need to check your gain staging. Overdriving inputs on digital is a bad thing and best avoided. A little more info about your set up may help.
Recently, there were several discussions on YouTube about how some people have been using audio plug-ins incorrectly. See linked video below. This is generally the main reason that there may be a difference between the software and hardware audio output.
Suffice to say that Helix Native software is the same as the firmware in the hardware unit, and the audio reproduction should be identical. The only things missing from Native are the physical hardware components, such as SEND/RETURN and the Looper. There should be no change whatsoever in the replayed tone.
Hope this helps/makes sense.