The Helix Floor and LT have aux inputs, but the impedance matching is not applied to that aux input. The Stomp and XL are the only units that apply it to both inputs, and I do use it a lot - often set ~136 hz. I run a second Stomp in the FX loop just for reverbs, since I use the dynamic split to shift between two parallel stereo reverbs. The Stomp produces enough latency that you will notice it if you use it for anything other than delays and reverbs, so I keep that second unit 100% wet and blend it on the first unit.
Well, it's not - it's not even consistent behavior from one effect to another. I can run a different phaser/flanger/chorus on each path and keep the pickups separate, no problem; switch one to a rotary cabinet and they're suddenly blended together (before the split). You were certainly right when you suggested using the stereo effects, but it doesn't work for every model, and that's not the behavior I would expect after using 5 generations of Line 6 modelers over the past 20 years.
They're less common now, but there were bi-amping bass combos that had a crossover built in, and that's easy to emulate with one input. And a number of famous custom rigs sent different pickups to different amps, and that's easy to do with the Y-split. Now I know these can be combined, even if it is definitely an edge case scenario. It does have a unique benefit of being able to really combine two different pickup sounds into one, rather than layering, and it works equally well on my fretless P-bass with a mudbucker in the neck, my Jaguar tuned from A to A in all 5ths, and my Tele-ish Godin Session Custom tuned down to C# standard. I've been using the Y-split for a few years, and it's pretty sweet to be able to save my pickup selection in each patch, flip the phase of a pickup with a footswitch, or switch from the neck to the bridge with an expression pedal.