I, too, am experiencing a lot of unusably distorted tones trying to use almost any Bass amp patch in Helix Native. The Ampeg SVT-4 PRO model is fair, but all others mostly are just unusably distorted. I can fight my way with the controls, such as reducing Drive, or playing with the cabs and mics to reduce the distortion, but I usually end up with really low levels and the results still don't sound right and worth the effort. I don't have any h/w Helix unit to compare, but I haven't had similar issues using Guitar patches with either a guitar or bass instrument. Results are as expected using other brand Bass amp models, such as NI Guitar Rig 5 or those provided with Logic X Pro 10.6.1. I'm using the latest HX Native v3.01, macOS Catalina, Presonus Quantum 2626 interface.
It seems as if something is broken somewhere in the gain structure. I hope Line 6 Moderators may consider this matter worthy of attention and having the developers address as needed.