Despite oversized stacks being possible as of Minecraft snapshot 24w12a, brewing stand slots will behave weirdly with said stacks:

• The fuel and input slots will both accept stacks of up to 64 initially then a higher stack.
• The three potion slots correctly accept up to 1 item each in most cases, though shift-clicking stacks of size 1 with a higher maximum size will still work to bypass the slot's size limit.

As a result of the last issue, multiple potions in a single stack can be brewed but will reset to size 1 and maximum size 1 after the brewing operation occurs. This reset technically results in the loss of potion items, but the operation should be illegal in the first place and is only possible due to the slot bug this issue describes.

I would expect all of this behavior to work consistently with both the maximum size of the stack and in the potion slots' case, the maximum size of the slot.

Code analysis (Yarn mappings)

The fuel and input slots have a defined maximum size of 64 in the BrewingStandScreenHandler.FuelSlot#getMaxItemCount and BrewingStandScreenHandler.IngredientSlot#getMaxItemCount methods respectively rather than the default Inventory#getMaxCountPerStack return value, which is correctly 99. The potion slot has a defined maximum size of 1 in the BrewingStandScreenHandler.PotionSlot#getMaxItemCount method.

All three of these slots seem to have a common issue that causes this value to be ignored.