Ender 3 v3 SE + Nebula Pad: Motherboard communication anomaly
If you - like I did - manage to brick your Creality Ender 3 v3 SE and you're using the Nebula Pad rather than the stock controller, then the instructions which Creality provide for resetting your firmware for this specific error are not quite right.
There are a separate set of firmware files which should be used in this instance.
The root cause to this issue was that I upgraded the Nebula Pad to v 1.1.0.27, which mistakenly sets the voltage to 0.6 rather than 0.8 causing a shift in layers during printing.
Before I was aware of the voltage issue in that firmware update, I had assumed the issue related to poor calibration. The print shown in the far left was the first attempt following the initial upgrade to the Nebula pad.
As I continued to experiment with infill settings and z-axis offsets, I wasn't actually getting any closer to a solution. Thankfully flashing the firmware Creality support recommended seems to have solved the issue.