I just tried to test this out, with meat and ham. And when i change the value for "preferred" in the cyclopedia, it updates in real time in the loot analyzer.
The supply analyzer however... does not update in real time and seems to only ever take market value or NPC value, which ever is greater
Even if i change the value, and clear the logging and reuse a pot, it still takes the market or NPC value, not my custom value.
I think you found a bug sir!