It would be nice if the custom food json would also allow for setting stack size for specific items.

I realized this as I was trying to trade rotten flesh to a villager who was asking for 36 flesh and flesh only stacks up to 16. I tried changing the food value or blacklisting it, but neither of those seem to allow for the standard vanilla stack size.

I ran into this issue as well.
Changing the villagers trades would be an option but that means that its less balanced and easier to get emeralds.

Yes, please. At least make it so the maximum stack size is still 64 and doesn't affect trade items. I use HO with Spice of Life, so being able to stack food to 64 really doesn't make a difference.