This isn’t an issue more so than working as intended, and the solution is in your post.
With passthrough, the C1 passes through the audio from your HDMI device for your Q950a to encode AND decode.
So when you’re switching from one HDMI device to another, or to the OS apps and back, the soundbar’s pre-amp is changing audio codecs, then sending the newly acquired signal to the subwoofer & rears causing the sub’s amp to switch codecs as well. The sudden flux of energy from the change causes the drivers to thump in the sub and the rears; this is called clipping.
The reason you hear no thump/pop from the bar itself is b/c it’s connected directly via HDMI, while the sub and rears connect wirelessly.
Keep the LG C1’s audio set to Auto. This happens across all brands of tvs and soundbars; VIZIO, Samsung, Sonos, LG…
A true fox will be to get yourself a true home theater audio system, forgoing a soundbar setup.