Using a pretty baseline, vanilla+ style set of mods. Nothing should conflict.
Some configuration settings do not seem to have an effect in-game, particularly the updgradeSlotCount setting. There may be others, but I noticed the issue with that one in particular.

Using version 1.21.1-3.21.1.1.82 with fabric 16.10

My mistake. Changing the configuration options did not take effect because the metadata associated with existing backpacks was not affected.