It was the LodDataBuilder's block culling logic. 'lossy compression - visually equal'
3 lines of code fixed it, by adding a new 'if' to avoid culling the last datapoint of a column
I know that it will not have that much of a performance improvement on high-end GPUs, but for humble ones like mine, it sure helps.
The merge request for Queued Chunk Updates now also includes this small fix.
Long story:
I've been trying to find where my bedrock layer went for the past month... In the process, I learnt about DH's logic way more than I would have liked. Hopefully, I can contribute with small fixes like this in the future that will benefit lower end GPUs