Auto-sort only triggers when the number of items in inventory increases. It's been like that since auto-sort was added.
So in the case of crafting Black Bread, you have the following in inventory:
[1] Fire Crystal x12
[2] Distilled Water x12
[3] Rock Salt x12
[4] Rye Flour
[5] Rye Flour
After crafting once it looks like this:
[1] Fire Crystal x11
[2] Distilled Water x11
[3] Rock Salt x11
[4] Rye Flour
[5] Black Bread x4
And after another synth, it looks like this:
[1] Fire Crystal x10
[2] Distilled Water x10
[3] Rock Salt x10
[4] Black Bread x4
[5] Black Bread x4
Notice how the number of items doesn't change? It's always 5 items before and after crafting, so auto-sort will not trigger.
Next up, you buy some extra Rock Salt x2 from NPC.
[1] Fire Crystal x10
[2] Distilled Water x10
[3] Rock Salt x10
[4] Black Bread x4
[5] Black Bread x4
[6] Rock Salt x2
This increases number of items from 5 to 6, and auto-sort triggers:
[1] Fire Crystal x10
[2] Distilled Water x10
[3] Rock Salt x12
[4] Black Bread x8