Welp, that sucks. I held out a little bit of hope there.
I think you're onto something there, too. I somehow missed the post from bether in February 2017:
I had an iPhone 6S, which had an A9 processor, and I've had the phantom clicks since day one. However, on my iPad Mini 4, which has an A8X - no clicks, ever.
For those who can't/won't read the PDF, the relevant part is this:
"The [newer iPhone] occasionally fails to send all of the audio data it should, to the plugged-in USB audio device. This causes (quasi) periodic clicks and dropouts in the audio and then the audio may stop, altogether."
This is by a manufacturer of a completely different product, but describes the exact same issue, so it does definitely seem like an Apple issue rather than a Line6 one. The issue was also first picked up by Silicon Labs and submitted to Apple as a bug, so there's a pretty strong reason to point at Apple being the issue.
Now, the interesting bit is kind of related to one of the very first posts I made - that it may be related to the downsampling/bitrate mismatch from 48kHz to 44.1kHz. As the PDF notes, all iOS video audio is at 48kHz, so I've been trying to figure out if there's a way to somehow use that to video yourself playing to get the audio you need. The best pseudo-idea I have is:
You need 2 devices and a mixer. And some time.
Plug one device with your DAW/multitrack/play-along track into your mixer, and have some headphones out for you to play along with;
Plug your guitar/bass/vox/drum output into the Sonic Port;
Plug your Sonic Port lightning cable into your second device, on which you're going to film yourself playing;
Run a headphone out from your Sonic Port into your mixer, so you can hear what you're playing, along with the rest of your track;
Hit record on your video, then hit play on your backing track, and play along.
What you should end up with is a video with your solo track on it. You can then import the audio from that video and line it up in your DAW (although you will have to do that manually).
it is the hackiest hack, but theoretically it should allow you to record via the Sonic Port without any more random pops & clicks (probably).