Since this is one of the threads I found when researching the same issue, and it, like the others, had no real resolution, I am re-posting what I figured out here:
There is a stunning lack of information on using FBV3 with Helix Native. Line 6 support just points you at a pretty worthless support article if you ask for help. So, I decided to just buy an FBV3 to see if I could get it to work and return it if I couldn't.
I've made some progress.
As far as I can tell, you need to think of the process in a few steps.
1. Map buttons and pedals on the FBV to particular MIDI continuous controllers (CCs) using the Line 6 FBV Control app.
2. Map those MIDI CCs to Helix Native "Switches" and "Knobs" in Logic.
3. Select those Helix Native "Switches" and "Knobs" as control sources for particular parameters in the Helix Native Plug-in.
It is absurd that there is no "Helix Native" configuration file for the FBV Control app that maps some sensible CCs to the physical buttons and pedals. I suggest loading the Blank.fbv provided with the app and starting from scratch. I assigned A-D to General Control 1-4 (CC 016-019) and FS 1-4 to General Control 5-8 (CC 080-083).
Once you've picked CCs, which is really pretty arbitrary, I'd pick the General Audio 12 control layout in Logic since it provides 12 on screen controls to Learn. Assign them to Helix Native Switches 1-8 and Knob 1 & 2, at least, using the pulldown under Parameter Mapping. Then pick one of the on-screen controls, press the Learn button by "External Assignment," click the physical button on the FBV3 a few times, and then click Learn again to turn it off. The CC you assigned to that physical button in FBV3 Control should now be mapped to the generic "Switch" for the plug-in. Then, pick an effect in the plug-in, click the Edit tab in the UI, right-click a parameter you want to control, choose Automation Assign, and pick the virtual Switch you Learned.
For using FBV3 switches to turn effects on and off, right-click the effect in the effect chain, choose Automation Bypass, and pick the Switch you want to use (e.g., Switch 1 to enable/disable a compressor).
I could only get this to work with "Automation Assign." I could not get it to work with "Controller Assign," where you directly choose a MIDI CC. I had to bounce through assigning the CC to a Switch/Knob and then assign the Switch/Knob as an Automation to the effect parameter.
I hope someone else can figure out how to do something useful with the Bank Select and Tap buttons on the FBV3. I haven't gotten that far yet.
I see no hope of assigning colors to the FBV3 buttons, but at least the red circle round each foot switch indicates on/off per effect.
Here's a screenshot showing the results of steps 1, 2, & 3 above:
