I used Helix for over 3 years, two of those spent on the road. Through the same cab IRs the amp modeling differences aren't as huge as some claim, but they're there. The Helix can sound great but I do agree that Fractal is a step up in sound, feel, and effects. The thing with Helix is that you have to fight it to get where you want, whereas with Fractal you can just pull up any amp model, set the knobs where you would set the knobs on the real amp, pull up 57+121 IRs for a cab that goes with the amp, and you instantly have a very usable recorded or live tone with zero tweaking, and it feels great, as far as cleaning up with the volume knob or breaking up as you dig in, etc. Helix makes you work for it, as the knobs absolutely do not correspond to their real-world counterparts, and there is this weird high end that you have to manage by messing with EQ, high cuts, cab settings, and the amp settings. The high end on the Fractal is so smooth and nice, you can get an amp bright without any "digital weirdness." It's hard to explain but people who have used a Helix and compared them through the same IRs will probably agree with me on the high end. Best way to test it is to reamp some dry guitar through corresponding amp models on both units running the same cab IRs. It's very obvious in a direct A/B test like that.
The Helix is $1700 so to me the FM3+FC6 is an absolute home run at $1500 if you don't need to run two amps.
Native has exactly the same processing as the hardware. Any differences people experience are due to differences in the interface. If you use a Helix or HX Stomp as your interface (so you're controlling for the impedance and AD conversion), and set the input of your Native track to USB 7 (so Native is seeing the raw guitar input signal), they sound identical.