I think this is a little bit reductive.
There are circumstances where having two completely independent signal paths is desirable. (For me, most of the time.) If you design the OS to present the pair of processors as one monolithic resource, sure it might be a little more intuitive for new users, but:
a) You increase latency. (And then TGP explodes...)
b) You complicate the process of building out presets for multiple instruments. (E.g. vocals via the phantom-powered XLR input on Helix Floor.)
The latter is especially problematic on HX and QC, where Send blocks are limited to 1/4" analog I/O for some reason. (I assume it's an insurmountable reason since neither Line 6 nor NDSP have managed to... surmount it.) The only way to get at XLR or USB audio is by way of reconfiguring each processors Input / Output blocks differently.
In any case, it's not as complicated as we're making it out to be. The only thing the user needs to understand is that the end of the top lanes needs to be routed into the beginning of the bottom lanes (if you’re just cramming one guitar signal through the entire Helix, as most guitarists will.) Even then most presets - and some templates - are already set up this way. And you often run out of screen space for amp/effect blocks before you run out of actual DSP power (unless you’re throwing a lot amps or poly effects in series) so the GUI is kind of self-explanatory in this regard.